Summary
The Debian Med Pure Blend contains 1337 packages which
are grouped by metapackages. Each metapackage will cause the
installation of packages for a specific topic. The following table lists
the metapackages of Debian Med
|
Tasks page
This is a list of the Tasks Debian Med is made of:
Table of contents
This metapackage will install Debian packages for use in molecular biology,
structural biology and other biological sciences.
Official Debian packages with high relevance
-
Abacas
-
close gaps in genomic alignments from short reads
-
Abpoa
-
adaptive banded Partial Order Alignment
-
Abyss
-
de novo, parallel, sequence assembler for short reads
-
Acedb-other
-
retrieval of DNA or protein sequences
-
Adapterremoval
-
rapid adapter trimming, identification, and read merging of gene sequences
-
Adun-core
-
Molecular Simulator
-
Aegean
-
integrated genome analysis toolkit
-
Aevol
-
digital genetics model to run Evolution Experiments in silico
-
Alien-hunter
-
Interpolated Variable Order Motifs to identify horizontally acquired DNA
-
Alter-sequence-alignment
-
genomic sequences ALignment Transformation EnviRonment
-
Altree
-
program to perform phylogeny-based association and localization analysis
-
Amap-align
-
Protein multiple alignment by sequence annealing
-
Ampliconnoise
-
removal of noise from 454 sequenced PCR amplicons
-
Andi
-
Efficient Estimation of Evolutionary Distances
-
Anfo
-
Short Read Aligner/Mapper from MPG
-
Any2fasta
-
convert various sequence formats to FASTA
-
Aragorn
-
tRNA and tmRNA detection in nucleotide sequences
-
Arden
-
specificity control for read alignments using an artificial reference
-
Ariba
-
Antibiotic Resistance Identification By Assembly
-
Art-nextgen-simulation-tools
-
simulation tools to generate synthetic next-generation sequencing reads
-
Artemis
-
genome browser and annotation tool
-
Artfastqgenerator
-
outputs artificial FASTQ files derived from a reference genome
-
Assembly-stats
-
get assembly statistics from FASTA and FASTQ files
-
Assemblytics
-
detect and analyze structural variants from a genome assembly
-
Atac
-
genome assembly-to-assembly comparison
-
Ataqv
-
ATAC-seq QC and visualization
-
Atropos
-
NGS read trimming tool that is specific, sensitive, and speedy
-
Augur
-
pipeline components for real-time virus analysis
-
Augustus
-
gene prediction in eukaryotic genomes
-
Autodock
-
analysis of ligand binding to protein structure
-
Autodock-vina
-
docking of small molecules to proteins
-
Autogrid
-
pre-calculate binding of ligands to their receptor
-
Avogadro
-
Molecular Graphics and Modelling System
-
Axe-demultiplexer
-
Trie-based DNA sequencing read demultiplexer
-
Baitfisher
-
software package for designing hybrid enrichment probes
-
Bali-phy
-
Bayesian Inference of Alignment and Phylogeny
-
Ballview
-
free molecular modeling and molecular graphics tool
-
Bamclipper
-
Remove gene-specific primer sequences from SAM/BAM alignments
-
Bamkit
-
tools for common BAM file manipulations
-
Bamtools
-
toolkit for manipulating BAM (genome alignment) files
-
Bandage
-
Bioinformatics Application for Navigating De novo Assembly Graphs Easily
-
Barrnap
-
rapid ribosomal RNA prediction
-
Bbmap
-
BBTools genomic aligner and other tools for short sequences
-
Bcalm
-
de Bruijn compaction in low memory
-
Bcftools
-
genomic variant calling and manipulation of VCF/BCF files
-
Beads
-
2-DE electrophoresis gel image spot detection
-
Beagle
-
Genotype calling, genotype phasing and imputation of ungenotyped markers
-
Beast-mcmc
-
Bayesian MCMC phylogenetic inference
-
Beast2-mcmc
-
Bayesian MCMC phylogenetic inference
-
Bedops
-
high-performance genomic feature operations
-
Bedtools
-
suite of utilities for comparing genomic features
-
Belvu
-
multiple sequence alignment viewer and phylogenetic tool
-
Berkeley-express
-
Streaming quantification for high-throughput sequencing
-
Bifrost
-
parallel construction, indexing and querying of de Bruijn graphs
-
Bio-eagle
-
Haplotype phasing within a genotyped cohort or using a phased reference panel
-
Bio-rainbow
-
clustering and assembling short reads for bioinformatics
-
Bio-tradis
-
analyse the output from TraDIS analyses of genomic sequences
-
Bio-vcf
-
domain specific language (DSL) for processing the VCF format
-
Bioawk
-
extension of awk for biological sequence analysis
-
Biobambam2
-
tools for early stage alignment file processing
-
Biosyntax
-
Syntax Highlighting for Computational Biology (metapackage)
-
Bitseq
-
Bayesian Inference of Transcripts from Sequencing Data
-
Blasr
-
mapping single-molecule sequencing reads
-
Blixem
-
interactive browser of sequence alignments
-
Bolt-lmm
-
Efficient large cohorts genome-wide Bayesian mixed-model association testing
-
Bowtie
-
Ultrafast memory-efficient short read aligner
-
Bowtie2
-
ultrafast memory-efficient short read aligner
-
Boxshade
-
Pretty-printing of multiple sequence alignments
-
Bppphyview
-
Bio++ Phylogenetic Viewer
-
Bppsuite
-
Bio++ program suite
-
Brig
-
BLAST Ring Image Generator
-
Btllib-tools
-
Bioinformatics Technology Lab common code library tools
-
Busco
-
benchmarking sets of universal single-copy orthologs
-
Bustools
-
program for manipulating BUS files for single cell RNA-Seq datasets
-
Bwa
-
Burrows-Wheeler Aligner
-
Canu
-
single molecule sequence assembler for genomes
-
Cassiopee
-
index and search tool in genomic sequences
-
Cat-bat
-
taxonomic classification of contigs and metagenome-assembled genomes (MAGs)
-
Cct
-
visually comparing bacterial, plasmid, chloroplast, or mitochondrial sequences
-
Cd-hit
-
suite of programs designed to quickly group sequences
-
Cdbfasta
-
Constant DataBase indexing and retrieval tools for multi-FASTA files
-
Centrifuge
-
rapid and memory-efficient system for classification of DNA sequences
-
Cgview
-
Circular Genome Viewer
-
Changeo
-
Repertoire clonal assignment toolkit (Python 3)
-
Chimeraslayer
-
detects likely chimeras in PCR amplified DNA
-
Chromhmm
-
Chromatin state discovery and characterization
-
Chromimpute
-
Large-scale systematic epigenome imputation
-
Cif-tools
-
Suite of tools to manipulate, validate and query mmCIF files
-
Circlator
-
circularize genome assemblies
-
Circos
-
plotter for visualizing data
-
Clearcut
-
extremely efficient phylogenetic tree reconstruction
-
Clonalframe
-
inference of bacterial microevolution using multilocus sequence data
-
Clonalframeml
-
Efficient Inference of Recombination in Whole Bacterial Genomes
-
Clonalorigin
-
inference of homologous recombination in bacteria using whole genome sequences
-
Clustalo
-
General-purpose multiple sequence alignment program for proteins
-
Clustalw
-
global multiple nucleotide or peptide sequence alignment
-
Clustalx
-
Multiple alignment of nucleic acid and protein sequences (graphical interface)
-
Cnvkit
-
Copy number variant detection from targeted DNA sequencing
-
Codonw
-
Correspondence Analysis of Codon Usage
-
Comet-ms
-
Tandem mass spectrometry (MS/MS) search engine
-
Concavity
-
predictor of protein ligand binding sites from structure and conservation
-
Conservation-code
-
protein sequence conservation scoring tool
-
Coot
-
model building program for macromolecular crystallography
-
Covtobed
-
convert the coverage track from a BAM file into a BED file
-
Crac
-
integrated RNA-Seq read analysis
-
Csb
-
Computational Structural Biology Toolbox (CSB)
-
Ctffind
-
fast and accurate defocus estimation from electron micrographs
-
Cutadapt
-
Clean biological sequences from high-throughput sequencing reads
-
Cutesv
-
comprehensive discovery of structural variations of genomic sequences
-
Daligner
-
local alignment discovery between long nucleotide sequencing reads
-
Damapper
-
long read to reference genome mapping tool
-
Datamash
-
statistics tool for command-line interface
-
Dawg
-
simulate the evolution of recombinant DNA sequences
-
Dazzdb
-
manage nucleotide sequencing read data
-
Deblur
-
deconvolution for Illumina amplicon sequencing
-
Deepnano
-
alternative basecaller for MinION reads of genomic sequences
-
Delly
-
Structural variant discovery by read analysis
-
Density-fitness
-
Calculates per-residue electron density scores
-
Dextractor
-
(d)extractor and compression command library
-
Dialign
-
Segment-based multiple sequence alignment
-
Dialign-tx
-
Segment-based multiple sequence alignment
-
Diamond-aligner
-
accelerated BLAST compatible local sequence aligner
-
Discosnp
-
discovering Single Nucleotide Polymorphism from raw set(s) of reads
-
Disulfinder
-
cysteines disulfide bonding state and connectivity predictor
-
Dnaclust
-
tool for clustering millions of short DNA sequences
-
Dnarrange
-
Method to find rearrangements in long DNA reads relative to a genome seq
-
Dotter
-
detailed comparison of two genomic sequences
-
Drop-seq-tools
-
analyzing Drop-seq data
-
Dssp
-
protein secondary structure assignment based on 3D structure
-
Dwgsim
-
short sequencing read simulator
-
E-mem
-
Efficient computation of Maximal Exact Matches for very large genomes
-
Ea-utils
-
command-line tools for processing biological sequencing data
-
Ecopcr
-
estimate PCR barcode primers quality
-
Edtsurf
-
triangulated mesh surfaces for protein structures
-
Eigensoft
-
reduction of population bias for genetic analyses
-
Elph
-
DNA/protein sequence motif finder
-
Embassy-domainatrix
-
Extra EMBOSS commands to handle domain classification file
-
Embassy-domalign
-
Extra EMBOSS commands for protein domain alignment
-
Embassy-domsearch
-
Extra EMBOSS commands to search for protein domains
-
Emboss
-
European molecular biology open software suite
-
Emmax
-
genetic mapping considering population structure
-
Estscan
-
ORF-independent detector of coding DNA sequences
-
Examl
-
Exascale Maximum Likelihood (ExaML) code for phylogenetic inference
-
Exonerate
-
generic tool for pairwise sequence comparison
-
Fasta3
-
tools for searching collections of biological sequences
-
Fastahack
-
utility for indexing and sequence extraction from FASTA files
-
Fastani
-
Fast alignment-free computation of whole-genome Average Nucleotide Identity
-
Fastaq
-
FASTA and FASTQ file manipulation tools
-
Fastdnaml
-
Tool for construction of phylogenetic trees of DNA sequences
-
Fastlink
-
faster version of pedigree programs of Linkage
-
Fastml
-
maximum likelihood ancestral amino-acid sequence reconstruction
-
Fastp
-
Ultra-fast all-in-one FASTQ preprocessor
-
Fastq-pair
-
Rewrites paired end fastq so all reads have a mate to separate out singletons
-
Fastqc
-
quality control for high throughput sequence data
-
Fastqtl
-
Quantitative Trait Loci (QTL) mapper in cis for molecular phenotypes
-
Fasttree
-
phylogenetic trees from alignments of nucleotide or protein sequences
-
Ffindex
-
simple index/database for huge amounts of small files
-
Figtree
-
graphical phylogenetic tree viewer
-
Filtlong
-
quality filtering tool for long reads of genome sequences
-
Fitgcp
-
fitting genome coverage distributions with mixture models
-
Flash
-
Fast Length Adjustment of SHort reads
-
Flexbar
-
flexible barcode and adapter removal for sequencing platforms
-
Flye
-
de novo assembler for single molecule sequencing reads using repeat graphs
-
Fml-asm
-
tool for assembling Illumina short reads in small regions
-
Freebayes
-
Bayesian haplotype-based polymorphism discovery and genotyping
-
Freecontact
-
fast protein contact predictor
-
Fsa
-
Fast Statistical Alignment of protein, RNA or DNA sequences
-
Fsm-lite
-
frequency-based string mining (lite)
-
Gamgi
-
General Atomistic Modelling Graphic Interface (GAMGI)
-
Garli
-
phylogenetic analysis of molecular sequence data using maximum-likelihood
-
Garlic
-
visualization program for biomolecules
-
Gasic
-
genome abundance similarity correction
-
Gatb-core
-
Genome Analysis Toolbox with de-Bruijn graph
-
Gbrowse
-
GMOD Generic Genome Browser
-
Gdpc
-
visualiser of molecular dynamic simulations
-
Gemma
-
Genome-wide Efficient Mixed Model Association
-
Genometester
-
toolkit for performing set operations on k-mer lists
-
Genomethreader
-
software tool to compute gene structure predictions
-
Genometools
-
versatile genome analysis toolkit
-
Genomicsdb-tools
-
sparse array storage library for genomics (tools)
-
Gentle
-
??? missing short description for package gentle :-(
-
Gff2aplot
-
pair-wise alignment-plots for genomic sequences in PostScript
-
Gff2ps
-
produces PostScript graphical output from GFF-files
-
Gffread
-
GFF/GTF format conversions, region filtering, FASTA sequence extraction
-
Ggd-utils
-
programs for use in ggd
-
Ghemical
-
GNOME molecular modelling environment
-
Ghmm
-
General Hidden-Markov-Model library - tools
-
Glam2
-
gapped protein motifs from unaligned sequences
-
Gmap
-
spliced and SNP-tolerant alignment for mRNA and short reads
-
Grabix
-
wee tool for random access into BGZF files
-
Graphlan
-
circular representations of taxonomic and phylogenetic trees
-
Grinder
-
Versatile omics shotgun and amplicon sequencing read simulator
-
Gromacs
-
Molecular dynamics simulator, with building and analysis tools
-
Gsort
-
sort genomic data
-
Gubbins
-
phylogenetic analysis of genome sequences
-
Gwama
-
Genome-Wide Association Meta Analysis
-
Harvest-tools
-
archiving and postprocessing for reference-compressed genomic multi-alignments
-
Hhsuite
-
sensitive protein sequence searching based on HMM-HMM alignment
-
Hilive
-
realtime alignment of Illumina reads
-
Hisat2
-
graph-based alignment of short nucleotide reads to many genomes
-
Hmmer
-
profile hidden Markov models for protein sequence analysis
-
Hmmer2
-
profile hidden Markov models for protein sequence analysis
-
Hyphy-mpi
-
Hypothesis testing using Phylogenies (MPI version)
-
Hyphy-pt
-
Hypothesis testing using Phylogenies (pthreads version)
-
Idba
-
iterative De Bruijn Graph short read assemblers
-
Igblast
-
Immunoglobulin and T cell receptor variable domain sequence analysis
-
Igdiscover
-
analyzes antibody repertoires to find new V genes
-
Igor
-
infers V(D)J recombination processes from sequencing data
-
Igv
-
Integrative Genomics Viewer
-
Indelible
-
powerful and flexible simulator of biological evolution
-
Infernal
-
inference of RNA secondary structural alignments
-
Insilicoseq
-
sequencing simulator producing realistic Illumina reads
-
Ipig
-
integrating PSMs into genome browser visualisations
-
Iqtree
-
efficient phylogenetic software by maximum likelihood
-
Iva
-
iterative virus sequence assembler
-
Jaligner
-
Smith-Waterman algorithm with Gotoh's improvement
-
Jalview
-
multiple alignment editor
-
Jellyfish
-
count k-mers in DNA sequences
-
Jellyfish1
-
count k-mers in DNA sequences
-
Jmodeltest
-
HPC selection of models of nucleotide substitution
-
Jmol
-
Molecular Viewer
-
Kalign
-
Global and progressive multiple sequence alignment
-
Kallisto
-
near-optimal RNA-Seq quantification
-
Kaptive
-
obtain information about K and O types for Klebsiella genome assemblies
-
Khmer
-
in-memory DNA sequence kmer counting, filtering & graph traversal
-
Kineticstools
-
detection of DNA modifications
-
King-probe
-
Evaluate and visualize protein interatomic packing
-
Kissplice
-
Detection of various kinds of polymorphisms in RNA-seq data
-
Kleborate
-
tool to screen Klebsiella genome assemblies
-
Kma
-
mapping genomic sequences to raw reads directly against redundant databases
-
Kmc
-
count kmers in genomic sequences
-
Kmer
-
suite of tools for DNA sequence analysis
-
Kmerresistance
-
correlates mapped genes with the predicted species of WGS samples
-
Kraken
-
assigning taxonomic labels to short DNA sequences
-
Kraken2
-
taxonomic classification system using exact k-mer matches
-
Lagan
-
highly parametrizable pairwise global genome sequence aligner
-
Lamarc
-
Likelihood Analysis with Metropolis Algorithm using Random Coalescence
-
Lamassemble
-
Merges overlapping "long" DNA reads into a consensus sequences
-
Lambda-align
-
Local Aligner for Massive Biological DatA
-
Lambda-align2
-
Local Aligner for Massive Biological DatA - v2
-
Last-align
-
genome-scale comparison of biological sequences
-
Lastz
-
pairwise aligning DNA sequences
-
Leaff
-
biological sequence library utilities and applications
-
Lefse
-
determine features of organisms, clades, taxonomic units, genes
-
Libpwiz-tools
-
ProteoWizard command line tools
-
Librg-utils-perl
-
parsers and format conversion utilities used by (e.g.) profphd
-
Libvcflib-tools
-
C++ library for parsing and manipulating VCF files (tools)
-
Lighter
-
fast and memory-efficient sequencing error corrector
-
Loki
-
MCMC linkage analysis on general pedigrees
-
Ltrsift
-
postprocessing and classification of LTR retrotransposons
-
Lucy
-
DNA sequence quality and vector trimming tool
-
Lumpy-sv
-
general probabilistic framework for structural variant discovery
-
Macs
-
Model-based Analysis of ChIP-Seq on short reads sequencers
-
Macsyfinder
-
detection of macromolecular systems in protein datasets
-
Maffilter
-
process genome alignment in the Multiple Alignment Format
-
Mafft
-
Multiple alignment program for amino acid or nucleotide sequences
-
Malt
-
sequence alignment and analysis tool to process sequencing data
-
Mapdamage
-
tracking and quantifying damage patterns in ancient DNA sequences
-
Mapsembler2
-
bioinformatics targeted assembly software
-
Maq
-
maps short fixed-length polymorphic DNA sequence reads to reference sequences
-
Maqview
-
graphical read alignment viewer for short gene sequences
-
Mash
-
fast genome and metagenome distance estimation using MinHash
-
Massxpert
-
transitional package for massxpert -> massxpert2
-
Mauve-aligner
-
multiple genome alignment
-
Mcaller
-
find methylation in nanopore reads
-
Mecat2
-
ultra-fast and accurate de novo assembly tools for SMRT reads
-
Megadepth
-
computes coverage from BigWig and BAM sequencing files
-
Megahit
-
ultra-fast and memory-efficient meta-genome assembler
-
Megan-ce
-
interactive tool to explore and analyse microbiome sequencing data
-
Melting
-
compute the melting temperature of nucleic acid duplex
-
Meryl
-
in- and out-of-core kmer counting and utilities
-
Metabat
-
robust statistical framework for reconstructing genomes from metagenomic data
-
Metaeuk
-
sensitive, high-throughput gene discovery and annotation for metagenomics
-
Metaphlan
-
Metagenomic Phylogenetic Analysis
-
Metastudent
-
predictor of Gene Ontology terms from protein sequence
-
Mhap
-
locality-sensitive hashing to detect long-read overlaps
-
Microbegps
-
explorative taxonomic profiling tool for metagenomic data
-
Microbiomeutil
-
Microbiome Analysis Utilities
-
Mindthegap
-
performs detection and assembly of DNA insertion variants in NGS read datasets
-
Minexpert2
-
MS^n mass spectrometric data visualization and mining (runtime)
-
Minia
-
short-read biological sequence assembler
-
Miniasm
-
ultrafast de novo assembler for long noisy DNA sequencing reads
-
Minimac4
-
Fast Imputation Based on State Space Reduction HMM
-
Minimap
-
tool for approximate mapping of long biosequences such as DNA reads
-
Minimap2
-
versatile pairwise aligner for genomic and spliced nucleotide sequences
-
Mipe
-
Tools to store PCR-derived data
-
Mira-assembler
-
Whole Genome Shotgun and EST Sequence Assembler
-
Mirtop
-
annotate miRNAs with a standard mirna/isomir naming
-
Mlv-smile
-
Find statistically significant patterns in sequences
-
Mmb
-
model the structure and dynamics of macromolecules
-
Mmseqs2
-
ultra fast and sensitive protein search and clustering
-
Mosdepth
-
BAM/CRAM depth calculation biological sequencing
-
Mothur
-
sequence analysis suite for research on microbiota
-
Mptp
-
single-locus species delimitation
-
Mrbayes
-
Bayesian Inference of Phylogeny
-
Multiqc
-
output integration for RNA sequencing across tools and samples
-
Mummer
-
Efficient sequence alignment of full genomes
-
Murasaki
-
homology detection tool across multiple large genomes
-
Murasaki-mpi
-
homology detection tool across multiple large genomes (MPI-version)
-
Muscle
-
Multiple alignment program of protein sequences
-
Muscle3
-
multiple alignment program of protein sequences
-
Mustang
-
multiple structural alignment of proteins
-
Nanofilt
-
filtering and trimming of long read sequencing data
-
Nanolyse
-
remove lambda phage reads from a fastq file
-
Nanook
-
pre- and post-alignment analysis of nanopore sequencing data
-
Nanopolish
-
consensus caller for nanopore sequencing data
-
Nanostat
-
statistics on long biological sequences
-
Nanosv
-
structural variant caller for nanopore data
-
Nast-ier
-
NAST-based DNA alignment tool
-
Ncbi-acc-download
-
download genome files from NCBI by accession
-
Ncbi-blast+
-
next generation suite of BLAST sequence search tools
-
Ncbi-blast+-legacy
-
NCBI Blast legacy call script
-
Ncbi-entrez-direct
-
NCBI Entrez utilities on the command line
-
Ncbi-epcr
-
Tool to test a DNA sequence for the presence of sequence tagged sites
-
Ncbi-seg
-
tool to mask segments of low compositional complexity in amino acid sequences
-
Ncbi-tools-bin
-
NCBI libraries for biology applications (text-based utilities)
-
Ncbi-tools-x11
-
NCBI libraries for biology applications (X-based utilities)
-
Ncl-tools
-
tools to deal with NEXUS files
-
Ncoils
-
coiled coil secondary structure prediction
-
Neobio
-
computes alignments of amino acid and nucleotide sequences
-
Ngmlr
-
CoNvex Gap-cost alignMents for Long Reads
-
Njplot
-
phylogenetic tree drawing program
-
Norsnet
-
tool to identify unstructured loops in proteins
-
Norsp
-
predictor of non-regular secondary structure
-
Ntcard
-
Streaming algorithm to estimate cardinality in genomics datasets
-
Nxtrim
-
Optimized trimming of Illumina mate pair reads
-
Obitools
-
programs to analyze NGS data in a DNA metabarcoding context
-
Openms
-
package for LC/MS data management and analysis
-
Optimir
-
Integrating genetic variations in miRNA alignment
-
Pal2nal
-
converts proteins to genomic DNA alignment
-
Paleomix
-
pipelines and tools for the processing of ancient and modern HTS data
-
Paml
-
Phylogenetic Analysis by Maximum Likelihood (PAML)
-
Paraclu
-
Parametric clustering of genomic and transcriptomic features
-
Parasail
-
Aligner based on libparasail
-
Parsinsert
-
Parsimonious Insertion of unclassified sequences into phylogenetic trees
-
Parsnp
-
rapid core genome multi-alignment
-
Patman
-
rapid alignment of short sequences to large databases
-
Pbdagcon
-
sequence consensus using directed acyclic graphs
-
Pbhoney
-
genomic structural variation discovery
-
Pbjelly
-
genome assembly upgrading tool
-
Pbsim
-
simulator for PacBio sequencing reads
-
Pbsuite
-
software for Pacific Biosciences sequencing data
-
Pdb2pqr
-
Preparation of protein structures for electrostatics calculations
-
Perlprimer
-
Graphical design of primers for PCR
-
Perm
-
efficient mapping of short reads with periodic spaced seeds
-
Pftools
-
build and search protein and DNA generalized profiles
-
Phast
-
phylogenetic analysis with space/time models
-
Phipack
-
PHI test and other tests of recombination
-
Phybin
-
binning/clustering newick trees by topology
-
Phylip
-
package of programs for inferring phylogenies
-
Phylonium
-
Fast and Accurate Estimation of Evolutionary Distances
-
Phyml
-
Phylogenetic estimation using Maximum Likelihood
-
Physamp
-
sample sequence alignment corresponding to phylogeny
-
Phyutility
-
simple analyses or modifications on both phylogenetic trees and data matrices
-
Phyx
-
UNIX-style phylogenetic analyses on trees and sequences
-
Picard-tools
-
Command line tools to manipulate SAM and BAM files
-
Picopore
-
lossless compression of Nanopore files
-
Pigx-rnaseq
-
pipeline for checkpointed and distributed RNA-seq analyses
-
Piler
-
genomic repeat analysis
-
Pilercr
-
software for finding CRISPR repeats
-
Pilon
-
automated genome assembly improvement and variant detection tool
-
Pinfish
-
Collection of tools to annotate genomes using long read transcriptomics data
-
Pique
-
software pipeline for performing genome wide association studies
-
Pirs
-
Profile based Illumina pair-end Reads Simulator
-
Pizzly
-
Identifies gene fusions in RNA sequencing data
-
Placnet
-
Plasmid Constellation Network project
-
Plasmidid
-
mapping-based, assembly-assisted plasmid identification tool
-
Plasmidomics
-
draw plasmids and vector maps with PostScript graphics export
-
Plasmidseeker
-
identification of known plasmids from whole-genome sequencing reads
-
Plast
-
Parallel Local Sequence Alignment Search Tool
-
Plink
-
whole-genome association analysis toolset
-
Plink1.9
-
whole-genome association analysis toolset
-
Plink2
-
whole-genome association analysis toolset
-
Plip
-
fully automated protein-ligand interaction profiler
-
Poa
-
Partial Order Alignment for multiple sequence alignment
-
Populations
-
population genetic software
-
Porechop
-
adapter trimmer for Oxford Nanopore reads
-
Poretools
-
toolkit for nanopore nucleotide sequencing data
-
Pplacer
-
phylogenetic placement and downstream analysis
-
Prank
-
Probabilistic Alignment Kit for DNA, codon and amino-acid sequences
-
Predictnls
-
prediction and analysis of protein nuclear localization signals
-
Presto
-
toolkit for processing B and T cell sequences
-
Prime-phylo
-
bayesian estimation of gene trees taking the species tree into account
-
Primer3
-
tool to design flanking oligo nucleotides for DNA amplification
-
Prinseq-lite
-
PReprocessing and INformation of SEQuence data (lite version)
-
Proalign
-
Probabilistic multiple alignment program
-
Probabel
-
Toolset for Genome-Wide Association Analysis
-
Probalign
-
multiple sequence alignment using partition function posterior probabilities
-
Probcons
-
PROBabilistic CONSistency-based multiple sequence alignment
-
Proda
-
multiple alignment of protein sequences
-
Prodigal
-
Microbial (bacterial and archaeal) gene finding program
-
Profbval
-
predictor of flexible/rigid protein residues from sequence
-
Profisis
-
prediction of protein-protein interaction sites from sequence
-
Profnet-bval
-
neural network architecture for profbval
-
Profnet-chop
-
neural network architecture for profchop
-
Profnet-con
-
neural network architecture for profcon
-
Profnet-isis
-
neural network architecture for profisis
-
Profnet-md
-
neural network architecture for metadisorder
-
Profnet-norsnet
-
neural network architecture for norsnet
-
Profnet-prof
-
neural network architecture for profacc
-
Profnet-snapfun
-
neural network architecture for snapfun
-
Profphd
-
secondary structure and solvent accessibility predictor
-
Profphd-net
-
neural network architecture for profphd
-
Profphd-utils
-
profphd helper utilities convert_seq and filter_hssp
-
Proftmb
-
per-residue prediction of bacterial transmembrane beta barrels
-
Progressivemauve
-
multiple genome alignment algorithms
-
Prokka
-
rapid annotation of prokaryotic genomes
-
Proteinortho
-
Detection of (Co-)orthologs in large-scale protein analysis
-
Prottest
-
selection of best-fit models of protein evolution
-
Provean
-
Protein Variation Effect Analyzer
-
Pscan-chip
-
ChIP-based identifcation of TF binding sites
-
Pscan-tfbs
-
search for transcription factor binding sites
-
Psortb
-
bacterial localization prediction tool
-
Pullseq
-
Extract sequence from a fasta or fastq
-
Pycoqc
-
computes metrics and generates Interactive QC plots
-
Pycorrfit
-
tool for fitting correlation curves on a logarithmic plot
-
Pyensembl
-
installs data from the Ensembl genome database
-
Pyfastx
-
fast random access to sequences from FASTA/Q file - command
-
Pymol
-
Molecular Graphics System
-
Pyscanfcs
-
scientific tool for perpendicular line scanning FCS
-
Python3-biomaj3-daemon
-
BioMAJ daemon library
-
Python3-bioxtasraw
-
process biological small angle scattering data
-
Python3-cogent3
-
framework for genomic biology
-
Python3-emperor
-
visualizing high-throughput microbial community data
-
Python3-geneimpacts
-
wraps command line tools to assess variants in gene sequences
-
Python3-gffutils
-
Work with GFF and GTF files in a flexible database framework
-
Python3-pairtools
-
Framework to process sequencing data from a Hi-C experiment
-
Python3-pybedtools
-
Python 3 wrapper around BEDTools for bioinformatics work
-
Python3-sqt
-
SeQuencing Tools for biological DNA/RNA high-throughput data
-
Python3-treetime
-
inference of time stamped phylogenies and ancestral reconstruction (Python 3)
-
Pyvcf
-
helper scripts for Variant Call Format (VCF) parser
-
Qcat
-
demultiplexing Oxford Nanopore reads from FASTQ files
-
Qcumber
-
quality control of genomic sequences
-
Qiime
-
Quantitative Insights Into Microbial Ecology
-
Qtltools
-
Tool set for molecular QTL discovery and analysis
-
Quicktree
-
Neighbor-Joining algorithm for phylogenies
-
Quorum
-
QUality Optimized Reads of genomic sequences
-
Qutemol
-
interactive visualization of macromolecules
-
R-bioc-annotate
-
BioConductor annotation for microarrays
-
R-bioc-biostrings
-
GNU R string objects representing biological sequences
-
R-bioc-bitseq
-
transcript expression inference and analysis for RNA-seq data
-
R-bioc-cner
-
CNE Detection and Visualization
-
R-bioc-cummerbund
-
tool for analysis of Cufflinks RNA-Seq output
-
R-bioc-deseq2
-
R package for RNA-Seq Differential Expression Analysis
-
R-bioc-ebseq
-
R package for RNA-Seq Differential Expression Analysis
-
R-bioc-edger
-
Empirical analysis of digital gene expression data in R
-
R-bioc-genefilter
-
methods for filtering genes from microarray experiments
-
R-bioc-geoquery
-
Get data from NCBI Gene Expression Omnibus (GEO)
-
R-bioc-hilbertvis
-
GNU R package to visualise long vector data
-
R-bioc-htsfilter
-
GNU R filter replicated high-throughput transcriptome sequencing data
-
R-bioc-impute
-
Imputation for microarray data
-
R-bioc-limma
-
linear models for microarray data
-
R-bioc-megadepth
-
BioCOnductor BigWig and BAM related utilities
-
R-bioc-mergeomics
-
Integrative network analysis of omics data
-
R-bioc-metagenomeseq
-
GNU R statistical analysis for sparse high-throughput sequencing
-
R-bioc-mofa
-
Multi-Omics Factor Analysis (MOFA)
-
R-bioc-multiassayexperiment
-
Software for integrating multi-omics experiments in BioConductor
-
R-bioc-mutationalpatterns
-
GNU R comprehensive genome-wide analysis of mutational processes
-
R-bioc-phyloseq
-
GNU R handling and analysis of high-throughput microbiome census data
-
R-bioc-rtracklayer
-
GNU R interface to genome browsers and their annotation tracks
-
R-bioc-scater
-
Single-Cell Analysis Toolkit for Gene Expression Data in R
-
R-bioc-tfbstools
-
GNU R Transcription Factor Binding Site (TFBS) Analysis
-
R-cran-adegenet
-
GNU R exploratory analysis of genetic and genomic data
-
R-cran-adephylo
-
GNU R exploratory analyses for the phylogenetic comparative method
-
R-cran-alakazam
-
Immunoglobulin Clonal Lineage and Diversity Analysis
-
R-cran-ape
-
GNU R package for Analyses of Phylogenetics and Evolution
-
R-cran-bio3d
-
GNU R package for biological structure analysis
-
R-cran-distory
-
GNU R distance between phylogenetic histories
-
R-cran-genabel
-
GNU R package for genome-wide SNP association analysis
-
R-cran-kaos
-
Encoding of Sequences Based on Frequency Matrix Chaos
-
R-cran-phangorn
-
GNU R package for phylogenetic analysis
-
R-cran-phytools
-
GNU R phylogenetic tools for comparative biology
-
R-cran-pscbs
-
R package: Analysis of Parent-Specific DNA Copy Numbers
-
R-cran-qtl
-
GNU R package for genetic marker linkage analysis
-
R-cran-rotl
-
GNU R interface to the 'Open Tree of Life' API
-
R-cran-samr
-
GNU R significance analysis of microarrays
-
R-cran-sdmtools
-
Species Distribution Modelling Tools
-
R-cran-seqinr
-
GNU R biological sequences retrieval and analysis
-
R-cran-seurat
-
Tools for Single Cell Genomics
-
R-cran-shazam
-
Immunoglobulin Somatic Hypermutation Analysis
-
R-cran-spp
-
GNU R ChIP-seq processing pipeline
-
R-cran-tcr
-
Advanced Data Analysis of Immune Receptor Repertoires
-
R-cran-tigger
-
Infers new Immunoglobulin alleles from Rep-Seq Data
-
R-cran-treespace
-
Statistical Exploration of Landscapes of Phylogenetic Trees
-
R-cran-tsne
-
t-distributed stochastic neighbor embedding for R (t-SNE)
-
R-cran-vegan
-
Community Ecology Package for R
-
R-cran-webgestaltr
-
find over-represented properties in gene lists
-
R-cran-wgcna
-
Weighted Correlation Network Analysis
-
R-other-ascat
-
Allele-Specific Copy Number Analysis of Tumours
-
R-other-mott-happy.hbrem
-
GNU R package for fine-mapping complex diseases
-
R-other-rajewsky-dropbead
-
Basic Exploration and Analysis of Drop-seq Data
-
Racon
-
consensus module for raw de novo DNA assembly of long uncorrected reads
-
Radiant
-
explore hierarchical metagenomic data with zoomable pie charts
-
Ragout
-
Reference-Assisted Genome Ordering UTility
-
Rambo-k
-
Read Assignment Method Based On K-mers
-
Rampler
-
module for sampling genomic sequences
-
Rapmap
-
rapid sensitive and accurate DNA read mapping via quasi-mapping
-
Rasmol
-
visualization of biological macromolecules
-
Raster3d
-
tools for generating images of proteins or other molecules
-
Rate4site
-
detector of conserved amino-acid sites
-
Raxml
-
Randomized Axelerated Maximum Likelihood of phylogenetic trees
-
Ray
-
de novo genome assemblies of next-gen sequencing data
-
Rdp-alignment
-
Ribosomal Database Project (RDP) alignment tools package
-
Rdp-classifier
-
extensible sequence classifier for fungal lsu, bacterial and archaeal 16s
-
Rdp-readseq
-
Ribosomal Database Project (RDP) sequence reading and writing
-
Readseq
-
Conversion between sequence formats
-
Readucks
-
Nanopore read de-multiplexer (read demux -> readux -> readucks, innit)
-
Reapr
-
universal tool for genome assembly evaluation
-
Recan
-
genetic distance plotting for recombination events analysis
-
Relion
-
toolkit for 3D reconstructions in cryo-electron microscopy
-
Relion-gui
-
toolkit for 3D reconstructions in cryo-electron microscopy (gui apps)
-
Repeatmasker-recon
-
finds repeat families from biological sequences
-
Reprof
-
protein secondary structure and accessibility predictor
-
Resfinder
-
identify acquired antimicrobial resistance genes
-
Rna-star
-
ultrafast universal RNA-seq aligner
-
Rnahybrid
-
Fast and effective prediction of microRNA/target duplexes
-
Roary
-
high speed stand alone pan genome pipeline
-
Rockhopper
-
system for analyzing bacterial RNA-seq data
-
Roguenarok
-
versatile and scalable algorithm for rogue taxon identification
-
Rsem
-
RNA-Seq by Expectation-Maximization
-
Rtax
-
Classification of sequence reads of 16S ribosomal RNA gene
-
Runcircos-gui
-
GUI tool to run circos
-
Saint
-
Significance Analysis of INTeractome
-
Salmid
-
rapid Kmer based Salmonella identifier from sequence data
-
Salmon
-
wicked-fast transcript quantification from RNA-seq data
-
Sambamba
-
tools for working with SAM/BAM data
-
Samblaster
-
marks duplicates, extracts discordant/split reads
-
Samclip
-
filter SAM file for soft and hard clipped alignments
-
Samtools
-
processing sequence alignments in SAM, BAM and CRAM formats
-
Savvy-util
-
conversion tool for SAV file format
-
Scoary
-
pangenome-wide association studies
-
Scrappie
-
basecaller for Nanopore sequencer
-
Scrm
-
simulator of evolution of genetic sequences
-
Scythe
-
Bayesian adaptor trimmer for sequencing reads
-
Seaview
-
Multiplatform interface for sequence alignment and phylogeny
-
Seer
-
genomic sequence element (kmer) enrichment analysis
-
Segemehl
-
short read mapping with gaps
-
Sepp
-
phylogeny with ensembles of Hidden Markov Models
-
Seqan-apps
-
C++ library for the analysis of biological sequences
-
Seqan-needle
-
pre-filter for the counting of very large collections of nucleotide sequences
-
Seqan-raptor
-
pre-filter for querying very large collections of nucleotide sequences
-
Seqkit
-
cross-platform and ultrafast toolkit for FASTA/Q file manipulation
-
Seqmagick
-
imagemagick-like frontend to Biopython SeqIO
-
Seqprep
-
stripping adaptors and/or merging paired reads of DNA sequences with overlap
-
Seqsero
-
Salmonella serotyping from genome sequencing data
-
Seqtk
-
Fast and lightweight tool for processing sequences in the FASTA or FASTQ format
-
Sga
-
de novo genome assembler that uses string graphs
-
Shasta
-
nanopore whole genome assembly (binaries and scripts)
-
Shovill
-
Assemble bacterial isolate genomes from Illumina paired-end reads
-
Sibelia
-
comparative genomics tool
-
Sibsim4
-
align expressed RNA sequences on a DNA template
-
Sickle
-
windowed adaptive trimming tool for FASTQ files using quality
-
Sigma-align
-
Simple greedy multiple alignment of non-coding DNA sequences
-
Sim4
-
tool for aligning cDNA and genomic DNA
-
Sim4db
-
batch spliced alignment of cDNA sequences to a target genome
-
Simka
-
comparative metagenomics method dedicated to NGS datasets
-
Simkamin
-
approximate comparative metagenomics method dedicated to NGS datasets
-
Ska
-
Split Kmer Analysis
-
Skesa
-
strategic Kmer extension for scrupulous assemblies
-
Skewer
-
post-processing of high-throughput DNA sequence reads
-
Smalt
-
Sequence Mapping and Alignment Tool
-
Smithwaterman
-
determine similar regions between two strings or genomic sequences
-
Smrtanalysis
-
software suite for single molecule, real-time sequencing
-
Snap
-
location of genes from DNA sequence with hidden markov model
-
Snap-aligner
-
Scalable Nucleotide Alignment Program
-
Sniffles
-
structural variation caller using third-generation sequencing
-
Snippy
-
rapid haploid variant calling and core genome alignment
-
Snp-sites
-
Binary code for the package snp-sites
-
Snpeff
-
genetic variant annotation and effect prediction toolbox - tool
-
Snpomatic
-
fast, stringent short-read mapping software
-
Snpsift
-
tool to annotate and manipulate genome variants - tool
-
Soapaligner
-
aligner of short reads of next generation sequencers
-
Soapdenovo
-
short-read assembly method to build de novo draft assembly
-
Soapdenovo2
-
short-read assembly method to build de novo draft assembly
-
Soapsnp
-
resequencing utility that can assemble consensus sequence of genomes
-
Sortmerna
-
tool for filtering, mapping and OTU-picking NGS reads
-
Spaced
-
alignment-free sequence comparison using spaced words
-
Spades
-
genome assembler for single-cell and isolates data sets
-
Spaln
-
splicing-aware transcript-alignment to genomic DNA
-
Spoa
-
SIMD partial order alignment tool
-
Sprai
-
single-pass sequencing read accuracy improver
-
Spread-phy
-
analyze and visualize phylogeographic reconstructions
-
Sra-toolkit
-
utilities for the NCBI Sequence Read Archive
-
Srst2
-
Short Read Sequence Typing for Bacterial Pathogens
-
Ssake
-
genomics application for assembling millions of very short DNA sequences
-
Sspace
-
scaffolding pre-assembled contigs after extension
-
Ssw-align
-
Smith-Waterman aligner based on libssw
-
Stacks
-
pipeline for building loci from short-read DNA sequences
-
Staden
-
DNA sequence assembly (Gap4/Gap5), editing and analysis tools
-
Staden-io-lib-utils
-
programs for manipulating DNA sequencing files
-
Stringtie
-
assemble short RNAseq reads to transcripts
-
Subread
-
toolkit for processing next-gen sequencing data
-
Suitename
-
categorize each suite in an RNA backbone
-
Sumaclust
-
fast and exact clustering of genomic sequences
-
Sumatra
-
fast and exact comparison and clustering of sequences
-
Sumtrees
-
Phylogenetic Tree Summarization and Annotation
-
Surankco
-
Supervised Ranking of Contigs in de novo Assemblies
-
Surpyvor
-
modification of VCF files with SURVIVOR
-
Survivor
-
tool set for simulating/evaluating SVs
-
Svim
-
Structural variant caller for long sequencing reads
-
Swarm
-
robust and fast clustering method for amplicon-based studies
-
Sweed
-
assessment of SNPs for their evolutionary advantage
-
T-coffee
-
Multiple Sequence Alignment
-
Tabix
-
generic indexer for TAB-delimited genome position files
-
Tantan
-
low complexity and tandem repeat masker for biosequences
-
Terraphast
-
enumerate terraces in phylogenetic tree space
-
Theseus
-
superimpose macromolecules using maximum likelihood
-
Thesias
-
Testing Haplotype Effects In Association Studies
-
Tiddit
-
structural variant calling
-
Tigr-glimmer
-
Gene detection in archea and bacteria
-
Tipp
-
tool for Taxonomic Identification and Phylogenetic Profiling
-
Tm-align
-
structural alignment of proteins
-
Tnseq-transit
-
statistical calculations of essentiality of genes or genomic regions
-
Toil
-
cross-platform workflow engine
-
Tombo
-
identification of modified nucleotides from raw nanopore sequencing data
-
Tophat
-
fast splice junction mapper for RNA-Seq reads
-
Tophat-recondition
-
post-processor for TopHat unmapped reads
-
Topp
-
set of programs implementing The OpenMS Proteomic Pipeline
-
Toppred
-
transmembrane topology prediction
-
Tortoize
-
Application to calculate ramachandran z-scores
-
Trace2dbest
-
bulk submission of chromatogram data to dbEST
-
Tracetuner
-
interpretation of DNA Sanger sequencing data
-
Transdecoder
-
find coding regions within RNA transcript sequences
-
Transrate-tools
-
helper for transrate
-
Transtermhp
-
find rho-independent transcription terminators in bacterial genomes
-
Tree-ppuzzle
-
Parallelized reconstruction of phylogenetic trees by maximum likelihood
-
Tree-puzzle
-
Reconstruction of phylogenetic trees by maximum likelihood
-
Treeview
-
Java re-implementation of Michael Eisen's TreeView
-
Treeviewx
-
Displays and prints phylogenetic trees
-
Trf
-
locate and display tandem repeats in DNA sequences
-
Trim-galore
-
automate quality and adapter trimming for DNA sequencing
-
Trimmomatic
-
flexible read trimming tool for Illumina NGS data
-
Trinityrnaseq
-
RNA-Seq De novo Assembly
-
Tvc
-
genetic variant caller for Ion Torrent sequencing platforms
-
Twopaco
-
build the compacted de Bruijn graph from many complete genomes
-
Uc-echo
-
error correction algorithm designed for short-reads from NGS
-
Ugene
-
integrated bioinformatics toolkit
-
Umap-learn
-
Uniform Manifold Approximation and Projection
-
Umis
-
tools for processing UMI RNA-tag data
-
Uncalled
-
Utility for Nanopore Current Alignment to Large Expanses of DNA
-
Unicycler
-
hybrid assembly pipeline for bacterial genomes
-
Unikmer
-
Toolkit for nucleic acid k-mer analysis
-
Varna
-
Visualization Applet for RNA
-
Vcfanno
-
annotate a VCF with other VCFs/BEDs/tabixed files
-
Vcftools
-
Collection of tools to work with VCF files
-
Velvet
-
Nucleic acid sequence assembler for very short reads
-
Velvet-long
-
Nucleic acid sequence assembler for very short reads, long version
-
Velvetoptimiser
-
automatically optimise Velvet do novo assembly parameters
-
Veryfasttree
-
Speeding up the estimation of phylogenetic trees from sequences
-
Vg
-
tools for working with genome variation graphs
-
Viewmol
-
graphical front end for computational chemistry programs
-
Virulencefinder
-
identify virulence genes in total or partial sequenced isolates of bacteria
-
Vmatch
-
large scale sequence analysis software
-
Vsearch
-
tool for processing metagenomic sequences
-
Vt
-
toolset for short variant discovery in genetic sequence data
-
Wham-align
-
Wisconsin's High-Throughput Alignment Method
-
Wigeon
-
reimplementation of the Pintail 16S DNA anomaly detection utility
-
Wise
-
comparison of biopolymers, like DNA and protein sequences
-
Xpore
-
Nanopore analysis of differential RNA modifications
-
Yaha
-
find split-read mappings on single-end queries
-
Yanagiba
-
filter low quality Oxford Nanopore reads basecalled with Albacore
-
Yanosim
-
read simulator nanopore DRS datasets
Official Debian packages with lower relevance
-
Adun.app
-
Molecular Simulator for GNUstep (GUI)
-
Catfishq
-
concatenates fastq files
-
Conda-package-handling
-
create and extract conda packages of various formats
-
Dascrubber
-
alignment-based scrubbing pipeline for DNA sequencing reads
-
Dnapi
-
adapter prediction for small RNA sequencing - utils
-
Emboss-explorer
-
web-based GUI to EMBOSS
-
Getdata
-
management of external databases
-
Hts-nim-tools
-
tools biological sequences: bam-filter, count-reads, vcf-check
-
Idseq-bench
-
Benchmark generator for the IDseq Portal
-
Illustrate
-
cartoonish representations of large biological molecules
-
Libhdf5-dev
-
HDF5 - development files - serial version
-
Libhnswlib-dev
-
fast approximate nearest neighbor search
-
Maude
-
high-performance logical framework
-
Metastudent-data
-
predictor of Gene Ontology terms from protein sequence - data files
-
Metastudent-data-2
-
predictor of Gene Ontology terms from protein sequence - data #2
-
Mrs
-
Information Retrieval System for Biomedical databanks
-
Python3-alignlib
-
edit and Hamming distances for biological sequences
-
Python3-anndata
-
annotated gene by sample numpy matrix
-
Python3-cgecore
-
Python3 module for the Center for Genomic Epidemiology
-
Python3-cyvcf2
-
VCF parser based on htslib (Python 3)
-
Python3-deeptools
-
platform for exploring biological deep-sequencing data
-
Python3-deeptoolsintervals
-
handlig GTF-like sequence-associated interal-annotation
-
Python3-htseq
-
Python3 high-throughput genome sequencing read analysis utilities
-
Python3-intake
-
lightweight package for finding and investigating data
-
Python3-loompy
-
access loom formatted files for bioinformatics
-
Python3-nanoget
-
extract information from Oxford Nanopore sequencing data and alignments
-
Python3-nanomath
-
simple math function for other Oxford Nanopore processing scripts
-
Python3-ncls
-
datastructure for interval overlap queries
-
Python3-py2bit
-
access to 2bit files
-
Python3-pybel
-
Biological Expression Language
-
Python3-pychopper
-
identify, orient and trim full-length Nanopore cDNA reads
-
Python3-pyfaidx
-
efficient random access to fasta subsequences for Python 3
-
Python3-pyflow
-
lightweight parallel task engine for Python
-
Python3-pyranges
-
2D representation of genomic intervals and their annotations
-
Python3-pyrle
-
run length arithmetic in Python
-
Python3-pysam
-
interface for the SAM/BAM sequence alignment and mapping format (Python 3)
-
Python3-tinyalign
-
numerical representation of differences between strings
-
Q2-alignment
-
QIIME 2 plugin for generating and manipulating alignments
-
Q2-cutadapt
-
QIIME 2 plugin to work with adapters in sequence data
-
Q2-dada2
-
QIIME 2 plugin to work with adapters in sequence data
-
Q2-demux
-
QIIME 2 plugin for demultiplexing of sequence reads
-
Q2-emperor
-
QIIME2 plugin for display of ordination plots
-
Q2-feature-classifier
-
QIIME 2 plugin supporting taxonomic classification
-
Q2-feature-table
-
QIIME 2 plugin supporting operations on feature tables
-
Q2-fragment-insertion
-
QIIME 2 plugin for fragment insertion
-
Q2-metadata
-
QIIME 2 plugin for working with and visualizing Metadata
-
Q2-phylogeny
-
QIIME 2 plugin for phylogeny
-
Q2-quality-control
-
QIIME 2 plugin for quality assurance of feature and sequence data
-
Q2-quality-filter
-
QIIME2 plugin for PHRED-based filtering and trimming
-
Q2-sample-classifier
-
QIIME 2 plugin for machine learning prediction of sample data
-
Q2-taxa
-
QIIME 2 plugin for working with feature taxonomy annotations
-
Q2-types
-
QIIME 2 plugin defining types for microbiome analysis
-
Q2cli
-
Click-based command line interface for QIIME 2
-
Q2templates
-
Design template package for QIIME 2 Plugins
-
R-bioc-annotationhub
-
GNU R client to access AnnotationHub resources
-
R-bioc-aroma.light
-
BioConductor methods normalization and visualization of microarray data
-
R-bioc-beachmat
-
I/O for several formats storing matrix data
-
R-bioc-biocneighbors
-
Nearest Neighbor Detection for Bioconductor Packages
-
R-bioc-biocsingular
-
Singular Value Decomposition for Bioconductor Packages
-
R-bioc-ctc
-
Cluster and Tree Conversion
-
R-bioc-dnacopy
-
R package: DNA copy number data analysis
-
R-bioc-ensembldb
-
GNU R utilities to create and use an Ensembl based annotation database
-
R-bioc-experimenthub
-
BioConductor client to access ExperimentHub resources
-
R-bioc-geneplotter
-
R package of functions for plotting genomic data
-
R-bioc-genomicalignments
-
BioConductor representation and manipulation of short genomic alignments
-
R-bioc-genomicfiles
-
Distributed computing by file or by range
-
R-bioc-genomicranges
-
BioConductor representation and manipulation of genomic intervals
-
R-bioc-go.db
-
annotation maps describing the entire Gene Ontology
-
R-bioc-grohmm
-
GRO-seq Analysis Pipeline
-
R-bioc-gviz
-
Plotting data and annotation information along genomic coordinates
-
R-bioc-isoformswitchanalyzer
-
Identify, Annotate and Visualize Alternative Splicing and
-
R-bioc-org.hs.eg.db
-
genome-wide annotation for Human
-
R-bioc-qusage
-
qusage: Quantitative Set Analysis for Gene Expression
-
R-bioc-savr
-
GNU R parse and analyze Illumina SAV files
-
R-bioc-singlecellexperiment
-
S4 Classes for Single Cell Data
-
R-bioc-structuralvariantannotation
-
Variant annotations for structural variants
-
R-bioc-tximport
-
transcript-level estimates for biological sequencing
-
R-cran-amap
-
Another Multidimensional Analysis Package
-
R-cran-biwt
-
biweight mean vector and covariance and correlation
-
R-cran-boolnet
-
assembling, analyzing and visualizing Boolean networks
-
R-cran-corrplot
-
Visualization of a Correlation Matrix
-
R-cran-dynamictreecut
-
Methods for Detection of Clusters in Hierarchical Clustering
-
R-cran-epir
-
GNU R Functions for analysing epidemiological data
-
R-cran-fitdistrplus
-
support fit of parametric distribution
-
R-cran-forecast
-
GNU R forecasting functions for time series and linear models
-
R-cran-gprofiler2
-
Interface to the 'g:Profiler' Toolset
-
R-cran-minerva
-
Maximal Information-Based Nonparametric Exploration
-
R-cran-optimalcutpoints
-
Computing Optimal Cutpoints in Diagnostic Tests
-
R-cran-parmigene
-
Parallel Mutual Information to establish Gene Networks
-
R-cran-pheatmap
-
GNU R package to create pretty heatmaps
-
R-cran-qqman
-
R package for visualizing GWAS results using Q-Q and manhattan plots
-
R-cran-rcpphnsw
-
R bindings for a Library for Approximate Nearest Neighbors
-
R-cran-rentrez
-
GNU R interface to the NCBI's EUtils API
-
R-cran-sctransform
-
Variance Stabilizing Transformations for Single Cell UMI Data
-
Resfinder-db
-
ResFinder database is a curated database of acquired resistance genes
-
Science-workflow
-
workflow management systems useful for scientific research
Debian packages in contrib or non-free
-
Arb
-
phylogenetic sequence analysis suite - main program
-
Bcbio
-
toolkit for analysing high-throughput sequencing data
-
Blimps-utils
-
blocks database improved searcher
-
Caftools
-
maintenance of DNA sequence assemblies
-
Cluster3
-
Reimplementation of the Eisen-clustering software
-
Cufflinks
-
Transcript assembly, differential expression and regulation for RNA-Seq
-
Embassy-phylip
-
EMBOSS conversions of the programs in the phylip package
-
Relion-cuda
-
parallel toolkit for 3D reconstructions in cryo-electron microscopy
-
Relion-gui-cuda
-
toolkit for 3D reconstructions in cryo-electron microscopy (gui apps)
-
Seq-gen
-
simulate the evolution of nucleotide or amino acid sequences
-
Seqcluster
-
analysis of small RNA in NGS data
-
Sift
-
predicts if a substitution in a protein has a phenotypic effect
-
Solvate
-
arranges water molecules around protein structures
-
Trnascan-se
-
detection of transfer RNA genes in genomic sequence
-
Varscan
-
variant detection in next-generation sequencing data
-
Vdjtools
-
framework for post-analysis of B/T cell repertoires
-
Vienna-rna
-
RNA sequence analysis
Debian packages in New queue (hopefully available soon)
-
Sourmash
-
tools for comparing DNA sequences with MinHash sketches
Packaging has started and developers might try the packaging code in VCS
-
Acacia
-
Error-corrector for pyrosequenced amplicon reads.
-
Agat
-
another GFF analysis toolkit
-
Amos-assembler
-
modular whole genome assembler
-
Apollo
-
genome annotation viewer and editor
-
Arvados
-
managing and analyzing biomedical big data
-
Axparafit
-
optimized statistical analysis of host-parasite coevolution
-
Axpcoords
-
highly optimized and parallelized porting of pcoords
-
Bagpipe
-
genomewide LD mapping
-
Bax2bam
-
Convert legacy PacBio Bax.H5, Bas.H5, and Ccs.H5 files to the new PacBio BAM format
-
Biceps
-
error-tolerant peptide identification
-
Bigsdb
-
Bacterial Isolate Genome Sequence Database
-
Bismark
-
bisulfite read mapper and methylation caller
-
Blat
-
BLAST-Like Alignment Tool
-
Blobology
-
tool set for the visualisation of genome assemblies
-
Braker
-
annotating protein coding genes in genomes.
-
Card-rgi
-
analysis of genome sequences using the Resistance Gene Identifier
-
Cellprofiler
-
quantitatively measure phenotypes from images automatically
-
Cinema
-
multi-sequence alignment editor and viewer
-
Condetri
-
straight-forward trimming of FASTQ sequences
-
Contrafold
-
CONditional TRAining for RNA Secondary Structure Prediction
-
Covpipe
-
pipeline to generate consensus sequences from NGS reads
-
Crossbow
-
Genotyping from short reads using cloud computing
-
Crux-toolkit
-
toolkit for tandem mass spectrometry analysis
-
Cytoscape
-
visualizing molecular interaction networks
-
Dazzle
-
Java-based DAS server
-
Deepbinner
-
demultiplexing barcoded Oxford Nanopore sequencing reads
-
Dendroscope
-
analyzing and visualizing rooted phylogenetic trees and networks
-
Diann
-
data-independent acquisition (DIA) proteomics data processing
-
Ecell
-
Concept and environment for constructing virtual cells on computers
-
Ensembl
-
basic Ensembl genome browser
-
Ensembl-vep
-
Variant Effect Predictor predicting the functional effects of genomic variants
-
Euler-sr
-
correcting errors in short gene sequence reads and assembling them
-
Euler2
-
de novo repeat classification and fragment assembly
-
Exabayes
-
bayesian phylogenetic tree inference for large-scale analyses
-
Ffp
-
Feature Frequency Profile Phylogeny
-
Fieldbioinformatics
-
pipeline with virus identification with Nanopore sequencer
-
Flappie
-
flip-flop basecaller for Oxford Nanopore reads
-
Forester
-
Graphical vizualiation tool Archaeopteryx
-
Galaxy
-
scientific workflow and data integration platform for computational biology
-
Gatk
-
The Genome Analysis Toolkit
-
Gerp++
-
identifies constrained elements in multiple alignments
-
Gramalign
-
multiple alignment of biological sequences
-
Graphbin
-
refined binning of metagenomic contigs using assembly graphs
-
Graphmap2
-
highly sensitive and accurate mapper for long, error-prone reads
-
Haploview
-
Analysis and visualization of LD and haplotype maps
-
Hawkeye
-
Interactive Visual Analytics Tool for Genome Assemblies
-
Htqc
-
Quality control and filtration for illumina sequencing data
-
Idefix
-
index checking for improved demultiplexing of NGS data
-
Inspect
-
mass-spectrometry database search tool
-
Jbrowse
-
genome browser with an AJAX-based interface
-
Kempbasu
-
significance tests for comparing digital gene expression profiles
-
Mach-haplotyper
-
Markov Chain based SNP haplotyper
-
Mage2tab
-
MAGE-MLv1 converter and visualiser
-
Manta
-
structural variant and indel caller for mapped sequencing data
-
Marginphase
-
simultaneous haplotyping and genotyping
-
Martj
-
distributed data integration system for biological data
-
Medaka
-
sequence correction provided by ONT Research
-
Meme
-
search for common motifs in DNA or protein sequences
-
Mesquite
-
modular system for evolutionary analysis
-
Metabit
-
analysing microbial profiles from high-throughput sequencing shotgun data
-
Modeller
-
Protein structure modeling by satisfaction of spatial restraints
-
Molekel
-
Advanced Interactive 3D-Graphics for Molecular Sciences
-
Mosaik-aligner
-
reference-guided aligner for next-generation sequencing
-
Mpsqed
-
alignment editor and multiplex pyrosequencing assay designer
-
Mugsy
-
multiple whole genome alignment tool
-
Mview
-
biological sequence alignment conversion
-
Nano-snakemake
-
detection of structural variants in genome sequencing data
-
Nanocall
-
Basecaller for Oxford Nanopore Sequencing Data
-
Nanocomp
-
compare multiple runs of long biological sequences
-
Nanoplot
-
plotting scripts for long read sequencing data
-
Ncbi-magicblast
-
RNA-seq mapping tool
-
Nextsv
-
automated structural variation detection for long-read sequencing
-
Ngila
-
global pairwise alignments with logarithmic and affine gap costs
-
Ngsqctoolkit
-
toolkit for the quality control of next generation sequencing data
-
Nw-align
-
global protein sequence alignment
-
Oases
-
de novo transcriptome assembler for very short reads
-
Omegamap
-
describing selection and recombination in sequences
-
Oncofuse
-
predicting oncogenic potential of gene fusions
-
Optitype
-
precision HLA typing from next-generation sequencing data
-
Paipline
-
Pipeline for the Automatic Identification of Pathogens
-
Pangolin
-
Phylogenetic Assignment of Named Global Outbreak LINeages
-
Partitionfinder
-
choses partitioning schemes and models of molecular evolution for sequence data
-
Patristic
-
Calculate patristic distances and comparing the components of genetic change
-
Pcma
-
fast and accurate multiple sequence alignment based on profile consistency
-
Phylophlan
-
microbial Tree of Life using 400 universal proteins
-
Phyloviz-core
-
phylogenetic inference and data visualization for sequence based typing methods
-
Pigx-scrnaseq
-
pipeline for checkpointed and distributed scRNA-seq analyses
-
Pipasic
-
Protein Abundance Correction in Metaproteomic Data
-
Plato
-
Analysis, translation, and organization of large-scale genetic data
-
Pomoxis
-
analysis components from Oxford Nanopore Research
-
Profit
-
Protein structure alignment
-
Psipred
-
protein secondary structure prediction
-
Pssh2
-
set of scripts for mapping protein sequence to structure
-
Pufferfish
-
Efficient index for the colored, compacted, de Bruijn graph
-
Purple
-
Picking Unique Relevant Peptides for viraL Experiments
-
Q2-composition
-
QIIME2 plugin for Compositional statistics
-
Q2-deblur
-
QIIME2 plugin to wrap the Deblur software for sequence quality control
-
Q2-diversity
-
QIIME2 plugin for core diversity analysis
-
Q2-gneiss
-
QIIME2 plugin for Compositional Data Analysis and Visualization
-
Q2-longitudinal
-
QIIME2 plugin for longitudinal studies and paired comparisons
-
Q2-vsearch
-
QIIME 2 plugin for clustering and dereplicating with vsearch
-
Qtlreaper
-
QTL analysis for expression data
-
Qualimap
-
evaluating next generation sequencing alignment data
-
Quast
-
Quality Assessment Tool for Genome Assemblies
-
R-bioc-mofa2
-
Multi-Omics Factor Analysis v2
-
R-bioc-org.mm.eg.db
-
genome wide annotation for Mouse
-
R-cran-drinsight
-
drug repurposing on transcriptome sequencing data
-
R-other-apmswapp
-
GNU R Pre- and Postprocessing For Affinity Purification Mass Spectrometry
-
R-other-fastbaps
-
A fast genetic clustering algorithm that approximates a Dirichlet Process Mixture model
-
Raxml-ng
-
phylogenetic tree inference tool which uses maximum-likelihood
-
Repeatmasker
-
screen DNA sequences for interspersed repeats
-
Roadtrips
-
case-control association testing with unknown population and pedigree structure
-
Rosa
-
Removal of Spurious Antisense in biological RNA sequences
-
Rsat
-
Regulatory Sequence Analysis Tools
-
Sailfish
-
RNA-seq expression estimation
-
Sap
-
Pairwise protein structure alignment via double dynamic programming
-
Seq-seq-pan
-
workflow for the SEQuential alignment of SEQuences
-
Seqwish
-
alignment to variation graph inducer
-
Signalalign
-
HMM-HDP models for MinION signal alignments
-
Sina
-
reference based multiple sequence alignment
-
Sistr
-
Salmonella In Silico Typing Resource (SISTR)
-
Situs
-
Modeling of atomic resolution structures into low-resolution density maps
-
Sparta
-
automated reference-based bacterial RNA-seq Transcriptome Analysis
-
Ssaha
-
Sequence Search and Alignment by Hashing Algorithm
-
Strap
-
Comfortable and intuitive protein alignment editor / viewer
-
Strap-base
-
essential files for the interactive alignment viewer and editor Strap
-
Strelka
-
strelka2 germline and somatic small variant caller
-
Tab2mage
-
submitting large microarray experiment datasets to public repository database
-
Tacg
-
command line program for finding patterns in nucleic acids
-
Tandem-genotypes
-
compare lengths of duplications in DNA sequences
-
Tide
-
SEQUEST Searching for Peptide Identification from Tandem Mass Spectra
-
Tigr-glimmer-mg
-
finding genes in environmental shotgun DNA sequences
-
Tn-seqexplorer
-
explore and analyze Tn-seq data for prokaryotic genomes
-
Ufasta
-
utility to manipulate fasta files
-
Umap
-
quantify genome and methylome mappability
-
Unc-fish
-
Fast Identification of Segmental Homology
-
Varmatch
-
robust matching of small genomic variant datasets
-
Vmd
-
presentation of traces of molecular dynamics runs
-
Zodiac-zeden
-
ZODIAC - Zeden's Organise DIsplay And Compute
Unofficial packages built by somebody else
-
Big-blast
-
Helper tool to run blast on large sequences
-
Estferret
-
processes, clusters and annotates EST data
-
Maxd
-
data warehouse and visualisation environment for genomic expression data
-
Migrate
-
estimation of population sizes and gene flow using the coalescent
-
Msatfinder
-
identification and characterization of microsatellites in a comparative genomic context
-
Oligoarrayaux
-
Prediction of Melting Profiles for Nucleic Acids
-
Partigene
-
generating partial gemomes
-
Pfaat
-
Protein Family Alignment Annotation Tool
-
Prot4est
-
EST protein translation suite
-
Python3-orange
-
Data mining framework
-
Qtlcart
-
map quantitative traits using a map of molecular markers
-
Rbs-finder
-
find ribosome binding sites(RBS)
-
Roche454ace2caf
-
convert GS20 or FLX assemblies into CAF format
-
Splitstree
-
Analyzing and Visualizing Evolutionary Data
-
Taverna
-
designing and executing myGrid workflows for bioinformatics
-
Taxinspector
-
browser for entries in the NCBI taxonomy
-
Tetra
-
tetranucleotide frequency calculator
No known packages available but some record of interest (WNPP bug)
-
Btk-core
-
biomolecule Toolkit C++ library
-
Mirbase
-
The microRNA sequence database
-
Phylowin
-
Graphical interface for molecular phylogenetic inference
No known packages available
-
Amoscmp
-
comparative genome assembly package
-
Annovar
-
annotate genetic variants detected from diverse genomes
-
Arachne
-
toolkit for Whole Genome Shotgun Assembly
-
Asap
-
organize the data associated with a genome
-
Bambus
-
hierarchical approach to building contig scaffolds
-
Cactus
-
-
Cdna-db
-
quality-control checking of finished cDNA clone sequences
-
Cmap
-
view comparisons of genetic and physical maps
-
Contralign
-
parameter learning framework for protein pairwise sequence alignment
-
Copycat
-
fast access to cophylogenetic analyses
-
E-hive
-
distributed processing system based on 'autonomous agents'
-
Exalt
-
phylogenetic generalized hidden Markov model for predicting alternatively spliced exons
-
Excavator
-
gene expression data clustering
-
Figaro
-
novel vector trimming software
-
Forge
-
genome assembler for mixed read types
-
Gbrowse-syn
-
Generic Synteny Browser
-
Genemark
-
family of gene prediction programs
-
Genesplicer
-
computational method for splice site prediction
-
Genetrack
-
genomic data storage and visualization framework
-
Genezilla
-
eukaryotic gene finder
-
Genographer
-
read data and reconstruct them into a gel image
-
Glimmerhmm
-
Eukaryotic Gene-Finding System
-
Gmv
-
comparative genome browser for Murasaki
-
Jigsaw
-
gene prediction using multiple sources of evidence
-
Maker2
-
annotate genomes and create genome databases
-
Metarep
-
JCVI Metagenomics Reports
-
Minimus
-
AMOS lightweight assembler
-
Mummergpu
-
High-throughput sequence alignment using Graphics Processing Units
-
Obo-edit
-
editor for biological ontologies
-
Operondb
-
detect and analyze conserved gene pairs
-
Phagefinder
-
heuristic computer program to identify prophage regions within bacterial genomes
-
Phpphylotree
-
draw phylogenetic trees
-
Phylographer
-
Graph Visualization Tool
-
Pyrophosphate-tools
-
for assembling and searching pyrophosphate sequence data
-
Rose
-
Region-Of-Synteny Extractor
-
Treebuilder3d
-
viewer of SAGE and other types of gene expression data
-
Tripal
-
collection of Drupal modules for genomic research
-
Twain
-
syntenic genefinder employing a Generalized Pair Hidden Markov Model
-
Uniprime
-
workflow-based platform for universal primer design
-
X-tandem-pipeline
-
peptide/protein identification from MS/MS mass spectra
This metapackage will install Debian packages which might be helpful
for development of applications for biological research.
Official Debian packages with high relevance
-
Bio-tradis
-
analyse the output from TraDIS analyses of genomic sequences
-
Biobambam2
-
tools for early stage alignment file processing
-
Bioperl
-
Perl tools for computational molecular biology
-
Bioperl-run
-
BioPerl wrappers: scripts
-
Biosquid
-
utilities for biological sequence analysis
-
Cwltool
-
Common Workflow Language reference implementation
-
Gffread
-
GFF/GTF format conversions, region filtering, FASTA sequence extraction
-
Goby-java
-
next-generation sequencing data and results analysis tool
-
Libace-perl
-
Object-Oriented Access to ACEDB Databases
-
Libai-fann-perl
-
Perl wrapper for the FANN library
-
Libbambamc-dev
-
Development files for reading and writing BAM (genome alignment) files
-
Libbamtools-dev
-
C++ API for manipulating BAM (genome alignment) files
-
Libbigwig-dev
-
C library for handling bigWig files - header files
-
Libbio-alignio-stockholm-perl
-
stockholm sequence input/output stream
-
Libbio-asn1-entrezgene-perl
-
parser for NCBI Entrez Gene and NCBI Sequence records
-
Libbio-chado-schema-perl
-
DBIx::Class layer for the Chado database schema
-
Libbio-cluster-perl
-
BioPerl cluster modules
-
Libbio-coordinate-perl
-
BioPerl modules for working with biological coordinates
-
Libbio-das-lite-perl
-
implementation of the BioDas protocol
-
Libbio-db-biofetch-perl
-
Database object interface to BioFetch retrieval
-
Libbio-db-embl-perl
-
Database object interface for EMBL entry retrieval
-
Libbio-db-hts-perl
-
Perl interface to the HTS library
-
Libbio-db-ncbihelper-perl
-
collection of routines useful for queries to NCBI databases
-
Libbio-db-seqfeature-perl
-
Normalized feature for use with Bio::DB::SeqFeature::Store
-
Libbio-eutilities-perl
-
BioPerl interface to the Entrez Programming Utilities (E-utilities)
-
Libbio-featureio-perl
-
Modules for reading, writing, and manipulating sequence features
-
Libbio-graphics-perl
-
Generate GD images of Bio::Seq objects
-
Libbio-mage-perl
-
Container module for classes in the MAGE package: MAGE
-
Libbio-mage-utils-perl
-
Extra modules for classes in the MAGE package: MAGE
-
Libbio-primerdesigner-perl
-
Perl module to design PCR primers using primer3 and epcr
-
Libbio-samtools-perl
-
Perl interface to SamTools library for DNA sequencing
-
Libbio-scf-perl
-
Perl extension for reading and writing SCF sequence files
-
Libbio-tools-phylo-paml-perl
-
Bioperl interface to the PAML suite
-
Libbio-tools-run-alignment-clustalw-perl
-
Bioperl interface to Clustal W
-
Libbio-tools-run-alignment-tcoffee-perl
-
Bioperl interface to T-Coffee
-
Libbio-tools-run-remoteblast-perl
-
Object for remote execution of the NCBI Blast via HTTP
-
Libbio-variation-perl
-
BioPerl variation-related functionality
-
Libbiojava-java
-
Java API to biological data and applications (default version)
-
Libbiojava6-java
-
Java API to biological data and applications (version 6)
-
Libbioparser-dev
-
library for parsing several formats in bioinformatics
-
Libblasr-dev
-
tools for aligning PacBio reads to target sequences (development files)
-
Libbpp-core-dev
-
Bio++ Core library development files
-
Libbpp-phyl-dev
-
Bio++ Phylogenetic library development files
-
Libbpp-phyl-omics-dev
-
Bio++ Phylogenetics library: genomics components (development files)
-
Libbpp-popgen-dev
-
Bio++ Population Genetics library development files
-
Libbpp-qt-dev
-
Bio++ Qt Graphic classes library development files
-
Libbpp-raa-dev
-
Bio++ Remote Acnuc Access library development files
-
Libbpp-seq-dev
-
Bio++ Sequence library development files
-
Libbpp-seq-omics-dev
-
Bio++ Sequence library: genomics components (development files)
-
Libcdk-java
-
Chemistry Development Kit (CDK) Java libraries
-
Libchado-perl
-
database schema and tools for genomic data
-
Libcifpp-dev
-
??? missing short description for package libcifpp-dev :-(
-
Libconsensuscore-dev
-
algorithms for PacBio multiple sequence consensus -- development files
-
Libdivsufsort-dev
-
libdivsufsort header files
-
Libedlib-dev
-
library for sequence alignment using edit distance (devel)
-
Libfast5-dev
-
library for reading Oxford Nanopore Fast5 files -- headers
-
Libfastahack-dev
-
library for indexing and sequence extraction from FASTA files (devel)
-
Libffindex0-dev
-
library for simple index/database for huge amounts of small files (development)
-
Libfml-dev
-
development headers for libfml
-
Libgatbcore-dev
-
development library of the Genome Analysis Toolbox
-
Libgclib-dev
-
header files for Genome Code Lib (GCLib)
-
Libgenome-dev
-
toolkit for developing bioinformatic related software (devel)
-
Libgenome-model-tools-music-perl
-
module for finding mutations of significance in cancer
-
Libgenome-perl
-
pipelines, tools, and data management for genomics
-
Libgenometools0-dev
-
development files for GenomeTools
-
Libgff-dev
-
GFF/GTF parsing from cufflinks as a library
-
Libgkarrays-dev
-
library to query large collection of NGS sequences (development)
-
Libgo-perl
-
perl modules for GO and other OBO ontologies
-
Libhdf5-dev
-
HDF5 - development files - serial version
-
Libhmsbeagle-dev
-
High-performance lib for Bayesian and Maximum Likelihood phylogenetics (devel)
-
Libhts-dev
-
development files for the HTSlib
-
Libhtscodecs-dev
-
Development headers for custom compression for CRAM and others
-
Libhtsjdk-java
-
Java API for high-throughput sequencing data (HTS) formats
-
Libjebl2-java
-
Java Evolutionary Biology Library
-
Libjloda-java
-
Java library of data structures and algorithms for bioinformatics
-
Libkmer-dev
-
suite of tools for DNA sequence analysis (development lib)
-
Libmems-dev
-
development library to support DNA string matching and comparative genomics
-
Libminimap2-dev
-
development headers for libminimap
-
Libmmblib-dev
-
development files of MacroMoleculeBuilder
-
Libmuscle-dev
-
multiple alignment development library for protein sequences
-
Libncbi-vdb-dev
-
libraries for using data in the INSDC Sequence Read Archives (devel)
-
Libncbi6-dev
-
NCBI libraries for biology applications (development files)
-
Libncl-dev
-
NEXUS Class Library (static lib and header files)
-
Libngs-java
-
Next Generation Sequencing language Bindings (Java bindings)
-
Libngs-sdk-dev
-
Next Generation Sequencing language Bindings (development)
-
Libnhgri-blastall-perl
-
Perl extension for running and parsing NCBI's BLAST 2.x
-
Libopenmm-dev
-
C++ header files for the OpenMM library
-
Libopenms-dev
-
library for LC/MS data management and analysis - dev files
-
Libpal-java
-
Phylogenetic Analysis Library
-
Libparasail-dev
-
Development heaaders and static libraries for parasail
-
Libpbbam-dev
-
Pacific Biosciences binary alignment/map (BAM) library (headers)
-
Libpbdata-dev
-
tools for handling PacBio sequences (development files)
-
Libpbihdf-dev
-
tools for handling PacBio hdf5 files (development files)
-
Libpbseq-dev
-
library for analyzing PacBio sequencing data (development files)
-
Libpdb-redo-dev
-
Development files for libpdb-redo
-
Libpll-dev
-
Phylogenetic Likelihood Library (development)
-
Libpwiz-dev
-
library to perform proteomics data analyses (devel files)
-
Libqes-dev
-
DNA sequence parsing library -- development
-
Librcsb-core-wrapper0-dev
-
development files for librcsb-core-wrapper0t64
-
Librdp-taxonomy-tree-java
-
taxonomy tree library from Ribosomal Database Project (RDP)
-
Librelion-dev
-
C++ API for RELION (3D reconstructions in cryo-electron microscopy)
-
Librg-blast-parser-perl
-
very fast NCBI BLAST parser - binding for Perl
-
Librg-reprof-bundle-perl
-
protein secondary structure and accessibility predictor (perl module)
-
Librostlab-blast0-dev
-
very fast C++ library for parsing the output of NCBI BLAST programs (devel)
-
Librostlab3-dev
-
C++ library for computational biology (development)
-
Libsbml5-dev
-
System Biology Markup Language library - development files
-
Libseqan2-dev
-
C++ library for the analysis of biological sequences (development)
-
Libseqan3-dev
-
C++ library for the analysis of biological sequences v3 (development)
-
Libseqlib-dev
-
C++ htslib/bwa-mem/fermi interface for interrogating sequence data (dev)
-
Libslow5-dev
-
header and static library for reading & writing SLOW5 files
-
Libsmithwaterman-dev
-
determine similar regions between two strings or genomic sequences (devel)
-
Libsnp-sites1-dev
-
Static libraries and header files for the package snp-sites
-
Libsort-key-top-perl
-
Perl module to select and sort top n elements of a list
-
Libspoa-dev
-
SIMD partial order alignment library (development files)
-
Libsrf-dev
-
C++ implementation of the SRF format for DNA sequence data
-
Libssm-dev
-
macromolecular superposition library - development files
-
Libssu-dev
-
high-performance phylogenetic diversity calculations (dev)
-
Libssw-dev
-
Development headers and static libraries for libssw
-
Libssw-java
-
Java bindings for libssw
-
Libstaden-read-dev
-
development files for libstaden-read
-
Libstatgen-dev
-
development files for the libStatGen
-
Libswiss-perl
-
Perl API to the UniProt database
-
Libtabixpp-dev
-
C++ wrapper to tabix indexer (development files)
-
Libthread-pool-dev
-
C++ header-only thread pool library (devel)
-
Libvcflib-dev
-
C++ library for parsing and manipulating VCF files (development)
-
Libvibrant6-dev
-
NCBI libraries for graphic biology applications (development files)
-
Libwfa2-dev
-
exact gap-affine algorithm (development)
-
Libzerg-perl
-
fast perl module for parsing the output of NCBI BLAST programs
-
Libzerg0-dev
-
development libraries and header files for libzerg
-
Mcl
-
Markov Cluster algorithm
-
Nim-hts-dev
-
wrapper for hts C library
-
Nim-kexpr-dev
-
kexpr math expressions for nim
-
Nim-lapper-dev
-
simple, fast interval searches for nim
-
Ont-fast5-api
-
simple interface to HDF5 files of the Oxford Nanopore .fast5 file format
-
Pyfai
-
Fast Azimuthal Integration scripts
-
Python3-airr
-
Data Representation Standard library for antibody and TCR sequences
-
Python3-anndata
-
annotated gene by sample numpy matrix
-
Python3-bcbio-gff
-
Python3 library to read and write Generic Feature Format
-
Python3-bioframe
-
library to enable flexible, scalable operations on genomic interval dataframes
-
Python3-biom-format
-
Biological Observation Matrix (BIOM) format (Python 3)
-
Python3-biomaj3
-
BioMAJ workflow management library
-
Python3-biopython
-
Python3 library for bioinformatics
-
Python3-biotools
-
??? missing short description for package python3-biotools :-(
-
Python3-bx
-
library to manage genomic data and its alignment
-
Python3-cgecore
-
Python3 module for the Center for Genomic Epidemiology
-
Python3-cigar
-
manipulate SAM cigar strings
-
Python3-cobra
-
constraint-based modeling of biological networks with Python 3
-
Python3-cogent3
-
framework for genomic biology
-
Python3-cooler
-
library for a sparse, compressed, binary persistent storage
-
Python3-corepywrap
-
library that exports C++ mmCIF accessors to Python3
-
Python3-csb
-
Python framework for structural bioinformatics (Python3 version)
-
Python3-cutadapt
-
Clean biological sequences from high-throughput sequencing reads (Python 3)
-
Python3-cyvcf2
-
VCF parser based on htslib (Python 3)
-
Python3-deeptools
-
platform for exploring biological deep-sequencing data
-
Python3-deeptoolsintervals
-
handlig GTF-like sequence-associated interal-annotation
-
Python3-dendropy
-
DendroPy Phylogenetic Computing Library (Python 3)
-
Python3-dnaio
-
Python 3 library for fast parsing of FASTQ and FASTA files
-
Python3-ete3
-
Python Environment for (phylogenetic) Tree Exploration - Python 3.X
-
Python3-fast5
-
library for reading Oxford Nanopore Fast5 files -- Python 3
-
Python3-freecontact
-
fast protein contact predictor - binding for Python3
-
Python3-gfapy
-
flexible and extensible software library for handling sequence graphs
-
Python3-gffutils
-
Work with GFF and GTF files in a flexible database framework
-
Python3-gtfparse
-
parser for gene transfer format (aka GFF2)
-
Python3-htseq
-
Python3 high-throughput genome sequencing read analysis utilities
-
Python3-intervaltree-bio
-
Interval tree convenience classes for genomic data -- Python 3 library
-
Python3-kineticstools
-
detection of DNA modifications (Python 3 library)
-
Python3-loompy
-
access loom formatted files for bioinformatics
-
Python3-mirtop
-
annotate miRNAs with a standard mirna/isomir naming (Python 3)
-
Python3-nanoget
-
extract information from Oxford Nanopore sequencing data and alignments
-
Python3-ngs
-
Next Generation Sequencing language Bindings (Python3 bindings)
-
Python3-pairix
-
1D/2D indexing and querying with a pair of genomic coordinates
-
Python3-pangolearn
-
store of the trained model for pangolin to access
-
Python3-parasail
-
Python3 bindings for the parasail C library
-
Python3-pbcommand
-
common command-line interface for Pacific Biosciences analysis modules
-
Python3-pbconsensuscore
-
algorithms for PacBio multiple sequence consensus -- Python 3
-
Python3-pbcore
-
Python 3 library for processing PacBio data files
-
Python3-peptidebuilder
-
generate atomic oligopeptide 3D structure from sequence
-
Python3-presto
-
toolkit for processing B and T cell sequences (Python3 module)
-
Python3-propka
-
heuristic pKa calculations with ligands (Python 3)
-
Python3-py2bit
-
access to 2bit files
-
Python3-pyabpoa
-
adaptive banded Partial Order Alignment - python3 module
-
Python3-pyani
-
Python3 module for average nucleotide identity analyses
-
Python3-pybedtools
-
Python 3 wrapper around BEDTools for bioinformatics work
-
Python3-pybel
-
Biological Expression Language
-
Python3-pybigwig
-
Python 3 module for quick access to bigBed and bigWig files
-
Python3-pyfaidx
-
efficient random access to fasta subsequences for Python 3
-
Python3-pyfastx
-
fast random access to sequences from FASTA/Q file - python3 module
-
Python3-pymummer
-
Python 3 interface to MUMmer
-
Python3-pyranges
-
2D representation of genomic intervals and their annotations
-
Python3-pysam
-
interface for the SAM/BAM sequence alignment and mapping format (Python 3)
-
Python3-pyspoa
-
Python bindings to spoa
-
Python3-pyvcf
-
Variant Call Format (VCF) parser for Python 3
-
Python3-rdkit
-
Collection of cheminformatics and machine-learning software
-
Python3-ruffus
-
Python3 computation pipeline library widely used in bioinformatics
-
Python3-screed
-
short nucleotide read sequence utils in Python 3
-
Python3-shasta
-
nanopore whole genome assembly (dynamic library)
-
Python3-skbio
-
Python3 data structures, algorithms, educational resources for bioinformatic
-
Python3-slow5
-
Python3 modul for reading & writing SLOW5 files
-
Python3-sqt
-
SeQuencing Tools for biological DNA/RNA high-throughput data
-
Python3-streamz
-
build pipelines to manage continuous streams of data
-
Python3-tinyalign
-
numerical representation of differences between strings
-
Python3-torch
-
Tensors and Dynamic neural networks in Python (Python Interface)
-
Python3-treetime
-
inference of time stamped phylogenies and ancestral reconstruction (Python 3)
-
Python3-unifrac
-
high-performance phylogenetic diversity calculations
-
Python3-wdlparse
-
Workflow Description Language (WDL) parser for Python
-
R-bioc-biobase
-
base functions for Bioconductor
-
R-cran-boolnet
-
assembling, analyzing and visualizing Boolean networks
-
R-cran-corrplot
-
Visualization of a Correlation Matrix
-
R-cran-distory
-
GNU R distance between phylogenetic histories
-
R-cran-fitdistrplus
-
support fit of parametric distribution
-
R-cran-forecast
-
GNU R forecasting functions for time series and linear models
-
R-cran-genetics
-
GNU R package for population genetics
-
R-cran-gprofiler2
-
Interface to the 'g:Profiler' Toolset
-
R-cran-haplo.stats
-
GNU R package for haplotype analysis
-
R-cran-phangorn
-
GNU R package for phylogenetic analysis
-
R-cran-pheatmap
-
GNU R package to create pretty heatmaps
-
R-cran-phylobase
-
GNU R base package for phylogenetic structures and comparative data
-
R-cran-pscbs
-
R package: Analysis of Parent-Specific DNA Copy Numbers
-
R-cran-qqman
-
R package for visualizing GWAS results using Q-Q and manhattan plots
-
R-cran-rentrez
-
GNU R interface to the NCBI's EUtils API
-
R-cran-rncl
-
GNU R interface to the Nexus Class Library
-
R-cran-rnexml
-
GNU R package for semantically rich I/O for the 'NeXML' format
-
R-cran-rotl
-
GNU R interface to the 'Open Tree of Life' API
-
R-cran-samr
-
GNU R significance analysis of microarrays
-
R-cran-sctransform
-
Variance Stabilizing Transformations for Single Cell UMI Data
-
R-cran-seqinr
-
GNU R biological sequences retrieval and analysis
-
R-cran-seurat
-
Tools for Single Cell Genomics
-
R-cran-tsne
-
t-distributed stochastic neighbor embedding for R (t-SNE)
-
R-cran-vegan
-
Community Ecology Package for R
-
R-cran-webgestaltr
-
find over-represented properties in gene lists
-
Ruby-bio
-
Ruby tools for computational molecular biology
-
Ruby-crb-blast
-
Run conditional reciprocal best blast
-
Sbmltoolbox
-
libsbml toolbox for octave and matlab
-
Snakemake
-
pythonic workflow management system
-
Toil
-
cross-platform workflow engine
Official Debian packages with lower relevance
-
Capsule-nextflow
-
packaging and deployment tool for Java applications
-
Conda-package-handling
-
create and extract conda packages of various formats
-
Ctdconverter
-
Convert CTD files into Galaxy tool and CWL CommandLineTool files
-
Cthreadpool-dev
-
minimal ANSI C thread pool - development files
-
Cwlformat
-
code formatter for Common Workflow Language
-
Cwltest
-
Common Workflow Language testing framework
-
Libargs-dev
-
simple header-only C++ argument parser library
-
Libbam-dev
-
manipulates nucleotide sequence alignments in BAM or SAM format
-
Libbbhash-dev
-
bloom-filter based minimal perfect hash function library
-
Libbifrost-dev
-
static library and header files for libbifrost
-
Libbiojava4-java
-
Java API to biological data and applications (default version)
-
Libbiosoup-dev
-
C++ header-only support library for bioinformatics tools
-
Libbtllib-dev
-
Bioinformatics Technology Lab common code library
-
Libcapsule-maven-nextflow-java
-
packaging tool for Java applications with Maven coordinates
-
Libconcurrentqueue-dev
-
industrial-strength lock-free queue for C++
-
Libdisorder-dev
-
library for entropy measurement of byte streams (devel)
-
Libfreecontact-dev
-
fast protein contact predictor library - development files
-
Libfreecontact-doc
-
documentation for libfreecontact
-
Libfreecontact-perl
-
fast protein contact predictor - binding for Perl
-
Libgatk-bwamem-java
-
interface to call Heng Li's bwa mem aligner from Java code
-
Libgatk-bwamem-jni
-
interface to call Heng Li's bwa mem aligner from Java code (jni)
-
Libgatk-fermilite-java
-
interface to call Heng Li's fermi-lite assembler from Java code
-
Libgatk-fermilite-jni
-
interface to call Heng Li's fermi-lite assembler from Java code (jni)
-
Libgatk-native-bindings-java
-
library of native bindings for gatk and picard-tools
-
Libgenomicsdb-dev
-
sparse array storage library for genomics (development files)
-
Libgenomicsdb-java
-
sparse array storage library for genomics (Java library)
-
Libicb-utils-java
-
Java library of utilities to manage files and compute statistics
-
Libmaus2-dev
-
collection of data structures and algorithms for biobambam (devel)
-
Libmilib-java
-
library for Next Generation Sequencing (NGS) data processing
-
Libminimap-dev
-
development headers for libminimap
-
Libmodhmm-dev
-
library for constructing, training and scoring hidden Markov models (dev)
-
Libpbcopper-dev
-
data structures, algorithms, and utilities for C++ applications -- header files
-
Librostlab-blast-doc
-
very fast C++ library for parsing the output of NCBI BLAST programs (doc)
-
Librostlab-doc
-
C++ library for computational biology (documentation)
-
Libsavvy-dev
-
C++ interface for the SAV file format
-
Libsuma-dev
-
headers and static library for sumatra and sumaclust
-
Libsvmloc-dev
-
PSORTb adapted library for svm machine-learning library (dev)
-
Libterraces-dev
-
enumerate terraces in phylogenetic tree space (development lib)
-
Libtfbs-perl
-
scanning DNA sequence with a position weight matrix
-
Libvbz-hdf-plugin-dev
-
VBZ compression plugin for nanopore signal data (devel)
-
Libxxsds-dynamic-dev
-
succinct and compressed fully-dynamic data structures library
-
Python-biopython-doc
-
Documentation for the Biopython library
-
Python3-alignlib
-
edit and Hamming distances for biological sequences
-
Python3-bel-resources
-
Python3 utilities for BEL resource files
-
Python3-bioblend
-
CloudMan and Galaxy API library (Python 3)
-
Python3-biopython-sql
-
Biopython support for the BioSQL database schema (Python 3)
-
Python3-cgelib
-
Python3 code to be utilized across the CGE tools
-
Python3-conda-package-streaming
-
fetch conda metadata
-
Python3-ctdopts
-
Gives your Python tools a CTD-compatible interface
-
Python3-intake
-
lightweight package for finding and investigating data
-
Python3-joypy
-
ridgeline-/joyplots plotting routine
-
Python3-ncls
-
datastructure for interval overlap queries
-
Python3-networkx
-
tool to create, manipulate and study complex networks (Python3)
-
Python3-pycosat
-
Python bindings to picosat
-
Python3-pyflow
-
lightweight parallel task engine for Python
-
Q2-alignment
-
QIIME 2 plugin for generating and manipulating alignments
-
Q2-cutadapt
-
QIIME 2 plugin to work with adapters in sequence data
-
Q2-dada2
-
QIIME 2 plugin to work with adapters in sequence data
-
Q2-demux
-
QIIME 2 plugin for demultiplexing of sequence reads
-
Q2-emperor
-
QIIME2 plugin for display of ordination plots
-
Q2-feature-classifier
-
QIIME 2 plugin supporting taxonomic classification
-
Q2-feature-table
-
QIIME 2 plugin supporting operations on feature tables
-
Q2-fragment-insertion
-
QIIME 2 plugin for fragment insertion
-
Q2-metadata
-
QIIME 2 plugin for working with and visualizing Metadata
-
Q2-phylogeny
-
QIIME 2 plugin for phylogeny
-
Q2-quality-control
-
QIIME 2 plugin for quality assurance of feature and sequence data
-
Q2-quality-filter
-
QIIME2 plugin for PHRED-based filtering and trimming
-
Q2-sample-classifier
-
QIIME 2 plugin for machine learning prediction of sample data
-
Q2-taxa
-
QIIME 2 plugin for working with feature taxonomy annotations
-
Q2-types
-
QIIME 2 plugin defining types for microbiome analysis
-
Q2cli
-
Click-based command line interface for QIIME 2
-
Q2templates
-
Design template package for QIIME 2 Plugins
-
Qiime
-
Quantitative Insights Into Microbial Ecology
-
R-bioc-affxparser
-
Affymetrix File Parsing SDK
-
R-bioc-affy
-
BioConductor methods for Affymetrix Oligonucleotide Arrays
-
R-bioc-affyio
-
BioConductor tools for parsing Affymetrix data files
-
R-bioc-altcdfenvs
-
BioConductor alternative CDF environments
-
R-bioc-annotate
-
BioConductor annotation for microarrays
-
R-bioc-annotationdbi
-
GNU R Annotation Database Interface for BioConductor
-
R-bioc-annotationhub
-
GNU R client to access AnnotationHub resources
-
R-bioc-aroma.light
-
BioConductor methods normalization and visualization of microarray data
-
R-bioc-arrayexpress
-
access to the ArrayExpress Microarray Database at EBI
-
R-bioc-biocgenerics
-
generic functions for Bioconductor
-
R-bioc-biocneighbors
-
Nearest Neighbor Detection for Bioconductor Packages
-
R-bioc-biomart
-
GNU R Interface to BioMart databases (Ensembl, COSMIC, Wormbase and Gramene)
-
R-bioc-biomformat
-
GNU R interface package for the BIOM file format
-
R-bioc-biostrings
-
GNU R string objects representing biological sequences
-
R-bioc-biovizbase
-
GNU R basic graphic utilities for visualization of genomic data
-
R-bioc-bitseq
-
transcript expression inference and analysis for RNA-seq data
-
R-bioc-bsgenome
-
BioConductor infrastructure for Biostrings-based genome data packages
-
R-bioc-cner
-
CNE Detection and Visualization
-
R-bioc-complexheatmap
-
make complex heatmaps using GNU R
-
R-bioc-ctc
-
Cluster and Tree Conversion
-
R-bioc-cummerbund
-
tool for analysis of Cufflinks RNA-Seq output
-
R-bioc-dada2
-
sample inference from amplicon sequencing data
-
R-bioc-deseq2
-
R package for RNA-Seq Differential Expression Analysis
-
R-bioc-dnacopy
-
R package: DNA copy number data analysis
-
R-bioc-ebseq
-
R package for RNA-Seq Differential Expression Analysis
-
R-bioc-ensembldb
-
GNU R utilities to create and use an Ensembl based annotation database
-
R-bioc-genefilter
-
methods for filtering genes from microarray experiments
-
R-bioc-geneplotter
-
R package of functions for plotting genomic data
-
R-bioc-genomeinfodb
-
BioConductor utilities for manipulating chromosome identifiers
-
R-bioc-genomicalignments
-
BioConductor representation and manipulation of short genomic alignments
-
R-bioc-genomicfeatures
-
GNU R tools for making and manipulating transcript centric annotations
-
R-bioc-genomicranges
-
BioConductor representation and manipulation of genomic intervals
-
R-bioc-geoquery
-
Get data from NCBI Gene Expression Omnibus (GEO)
-
R-bioc-go.db
-
annotation maps describing the entire Gene Ontology
-
R-bioc-graph
-
handle graph data structures for BioConductor
-
R-bioc-gseabase
-
Gene set enrichment data structures and methods
-
R-bioc-gsva
-
Gene Set Variation Analysis for microarray and RNA-seq data
-
R-bioc-gviz
-
Plotting data and annotation information along genomic coordinates
-
R-bioc-hypergraph
-
BioConductor hypergraph data structures
-
R-bioc-impute
-
Imputation for microarray data
-
R-bioc-iranges
-
GNU R low-level containers for storing sets of integer ranges
-
R-bioc-limma
-
linear models for microarray data
-
R-bioc-makecdfenv
-
BioConductor CDF Environment Maker
-
R-bioc-mergeomics
-
Integrative network analysis of omics data
-
R-bioc-metagenomeseq
-
GNU R statistical analysis for sparse high-throughput sequencing
-
R-bioc-mofa
-
Multi-Omics Factor Analysis (MOFA)
-
R-bioc-multiassayexperiment
-
Software for integrating multi-omics experiments in BioConductor
-
R-bioc-nanostringqcpro
-
??? missing short description for package r-bioc-nanostringqcpro :-(
-
R-bioc-oligo
-
Preprocessing tools for oligonucleotide arrays
-
R-bioc-oligoclasses
-
Classes for high-throughput arrays supported by oligo and crlmm
-
R-bioc-org.hs.eg.db
-
genome-wide annotation for Human
-
R-bioc-pcamethods
-
BioConductor collection of PCA methods
-
R-bioc-phyloseq
-
GNU R handling and analysis of high-throughput microbiome census data
-
R-bioc-preprocesscore
-
BioConductor collection of pre-processing functions
-
R-bioc-purecn
-
copy number calling and SNV classification using targeted short read sequencing
-
R-bioc-qusage
-
qusage: Quantitative Set Analysis for Gene Expression
-
R-bioc-rbgl
-
R interface to the graph algorithms contained in the BOOST library
-
R-bioc-rsamtools
-
GNU R binary alignment (BAM), variant call (BCF), or tabix file import
-
R-bioc-rtracklayer
-
GNU R interface to genome browsers and their annotation tracks
-
R-bioc-s4vectors
-
BioConductor S4 implementation of vectors and lists
-
R-bioc-savr
-
GNU R parse and analyze Illumina SAV files
-
R-bioc-shortread
-
GNU R classes and methods for high-throughput short-read sequencing data
-
R-bioc-snpstats
-
BioConductor SnpMatrix and XSnpMatrix classes and methods
-
R-bioc-structuralvariantannotation
-
Variant annotations for structural variants
-
R-bioc-tfbstools
-
GNU R Transcription Factor Binding Site (TFBS) Analysis
-
R-bioc-titancna
-
Subclonal copy number and LOH prediction from whole genome sequencing
-
R-bioc-tximport
-
transcript-level estimates for biological sequencing
-
R-bioc-variantannotation
-
BioConductor annotation of genetic variants
-
R-bioc-xvector
-
BioConductor representation and manpulation of external sequences
-
R-cran-adegenet
-
GNU R exploratory analysis of genetic and genomic data
-
R-cran-adephylo
-
GNU R exploratory analyses for the phylogenetic comparative method
-
R-cran-amap
-
Another Multidimensional Analysis Package
-
R-cran-biwt
-
biweight mean vector and covariance and correlation
-
R-cran-dt
-
GNU R wrapper of the JavaScript library 'DataTables'
-
R-cran-dynamictreecut
-
Methods for Detection of Clusters in Hierarchical Clustering
-
R-cran-fastcluster
-
Fast hierarchical clustering routines for GNU R
-
R-cran-future.apply
-
apply function to elements in parallel using futures
-
R-cran-future.batchtools
-
Future API for Parallel and Distributed Processing
-
R-cran-ica
-
Independent Component Analysis
-
R-cran-itertools
-
Iterator Tools
-
R-cran-kaos
-
Encoding of Sequences Based on Frequency Matrix Chaos
-
R-cran-metap
-
Meta-Analysis of Significance Values
-
R-cran-minerva
-
Maximal Information-Based Nonparametric Exploration
-
R-cran-natserv
-
GNU R 'NatureServe' Interface
-
R-cran-nmf
-
GNU R framework to perform non-negative matrix factorization
-
R-cran-optimalcutpoints
-
Computing Optimal Cutpoints in Diagnostic Tests
-
R-cran-parmigene
-
Parallel Mutual Information to establish Gene Networks
-
R-cran-pcapp
-
Robust PCA by Projection Pursuit
-
R-cran-proc
-
Display and Analyze ROC Curves
-
R-cran-rann
-
Fast Nearest Neighbour Search Using L2 Metric
-
R-cran-rcpphnsw
-
R bindings for a Library for Approximate Nearest Neighbors
-
R-cran-robustrankaggreg
-
Methods for robust rank aggregation
-
R-cran-rocr
-
GNU R package to prepare and display ROC curves
-
R-cran-rook
-
web server interface for R
-
R-cran-rsvd
-
Randomized Singular Value Decomposition
-
R-cran-shazam
-
Immunoglobulin Somatic Hypermutation Analysis
-
R-cran-sitmo
-
GNU R parallel pseudo random number generator 'sitmo' header files
-
R-cran-venndiagram
-
Generate High-Resolution Venn and Euler Plots
-
Ruby-rgfa
-
parse, edit and write GFA format graphs in Ruby
Debian packages in contrib or non-free
-
Python3-bcbio
-
library for analysing high-throughput sequencing data
-
Python3-seqcluster
-
analysis of small RNA in NGS data
-
Vdjtools
-
framework for post-analysis of B/T cell repertoires
Packaging has started and developers might try the packaging code in VCS
-
Libatomicqueue-dev
-
devel files for C++ atomic_queue library
-
Libfast-perl
-
FAST Analysis of Sequences Toolbox
-
Libforester-java
-
Libraries for evolutionary biology and comparative genomics research
-
Libnexml-java
-
Java API for NeXML
-
Python3-compclust
-
explore and quantify relationships between clustering results
-
Python3-consensuscore2
-
generate consensus sequences for PacBio data -- Python 3
-
Python3-galaxy-lib
-
Subset of Galaxy core code base designed to be used
-
Python3-misopy
-
Mixture of Isoforms model for RNA-Seq isoform quantitation (Python 3)
-
Python3-scanpy
-
Single-Cell Analysis in Python
-
Q2-composition
-
QIIME2 plugin for Compositional statistics
-
Q2-deblur
-
QIIME2 plugin to wrap the Deblur software for sequence quality control
-
Q2-diversity
-
QIIME2 plugin for core diversity analysis
-
Q2-gneiss
-
QIIME2 plugin for Compositional Data Analysis and Visualization
-
Q2-longitudinal
-
QIIME2 plugin for longitudinal studies and paired comparisons
-
Q2-vsearch
-
QIIME 2 plugin for clustering and dereplicating with vsearch
-
R-bioc-bridgedbr
-
identifier mapping between biological databases
-
R-cran-drinsight
-
drug repurposing on transcriptome sequencing data
-
R-other-apmswapp
-
GNU R Pre- and Postprocessing For Affinity Purification Mass Spectrometry
No known packages available
-
Bioclipse
-
platform for chemo- and bioinformatics based on Eclipse
-
Octace-bioinfo
-
Bioinformatics manipulation for Octave
It aims at gettting packages which specialize in the processing or interpretation of
data generated with next- (and later-) generation high-thoughput sequencing technologies.
Official Debian packages with high relevance
-
Anfo
-
Short Read Aligner/Mapper from MPG
-
Arden
-
specificity control for read alignments using an artificial reference
-
Art-nextgen-simulation-tools
-
simulation tools to generate synthetic next-generation sequencing reads
-
Artfastqgenerator
-
outputs artificial FASTQ files derived from a reference genome
-
Bamtools
-
toolkit for manipulating BAM (genome alignment) files
-
Bcftools
-
genomic variant calling and manipulation of VCF/BCF files
-
Bedtools
-
suite of utilities for comparing genomic features
-
Berkeley-express
-
Streaming quantification for high-throughput sequencing
-
Bio-rainbow
-
clustering and assembling short reads for bioinformatics
-
Blasr
-
mapping single-molecule sequencing reads
-
Bowtie
-
Ultrafast memory-efficient short read aligner
-
Bowtie2
-
ultrafast memory-efficient short read aligner
-
Bwa
-
Burrows-Wheeler Aligner
-
Canu
-
single molecule sequence assembler for genomes
-
Changeo
-
Repertoire clonal assignment toolkit (Python 3)
-
Crac
-
integrated RNA-Seq read analysis
-
Cutadapt
-
Clean biological sequences from high-throughput sequencing reads
-
Daligner
-
local alignment discovery between long nucleotide sequencing reads
-
Deepnano
-
alternative basecaller for MinION reads of genomic sequences
-
Discosnp
-
discovering Single Nucleotide Polymorphism from raw set(s) of reads
-
Dnaclust
-
tool for clustering millions of short DNA sequences
-
Dwgsim
-
short sequencing read simulator
-
Ea-utils
-
command-line tools for processing biological sequencing data
-
Fastaq
-
FASTA and FASTQ file manipulation tools
-
Fastp
-
Ultra-fast all-in-one FASTQ preprocessor
-
Fastqc
-
quality control for high throughput sequence data
-
Flexbar
-
flexible barcode and adapter removal for sequencing platforms
-
Fml-asm
-
tool for assembling Illumina short reads in small regions
-
Fsm-lite
-
frequency-based string mining (lite)
-
Giira
-
RNA-Seq driven gene finding incorporating ambiguous reads
-
Grinder
-
Versatile omics shotgun and amplicon sequencing read simulator
-
Hilive
-
realtime alignment of Illumina reads
-
Hinge
-
long read genome assembler based on hinging
-
Hisat2
-
graph-based alignment of short nucleotide reads to many genomes
-
Idba
-
iterative De Bruijn Graph short read assemblers
-
Igdiscover
-
analyzes antibody repertoires to find new V genes
-
Igor
-
infers V(D)J recombination processes from sequencing data
-
Igv
-
Integrative Genomics Viewer
-
Iva
-
iterative virus sequence assembler
-
Khmer
-
in-memory DNA sequence kmer counting, filtering & graph traversal
-
Kissplice
-
Detection of various kinds of polymorphisms in RNA-seq data
-
Kraken
-
assigning taxonomic labels to short DNA sequences
-
Kraken2
-
taxonomic classification system using exact k-mer matches
-
Last-align
-
genome-scale comparison of biological sequences
-
Libvcflib-tools
-
C++ library for parsing and manipulating VCF files (tools)
-
Macs
-
Model-based Analysis of ChIP-Seq on short reads sequencers
-
Mapdamage
-
tracking and quantifying damage patterns in ancient DNA sequences
-
Mapsembler2
-
bioinformatics targeted assembly software
-
Maq
-
maps short fixed-length polymorphic DNA sequence reads to reference sequences
-
Maqview
-
graphical read alignment viewer for short gene sequences
-
Mhap
-
locality-sensitive hashing to detect long-read overlaps
-
Microbiomeutil
-
Microbiome Analysis Utilities
-
Mira-assembler
-
Whole Genome Shotgun and EST Sequence Assembler
-
Mothur
-
sequence analysis suite for research on microbiota
-
Nanopolish
-
consensus caller for nanopore sequencing data
-
Paleomix
-
pipelines and tools for the processing of ancient and modern HTS data
-
Pbhoney
-
genomic structural variation discovery
-
Pbjelly
-
genome assembly upgrading tool
-
Pbsuite
-
software for Pacific Biosciences sequencing data
-
Picard-tools
-
Command line tools to manipulate SAM and BAM files
-
Pirs
-
Profile based Illumina pair-end Reads Simulator
-
Pizzly
-
Identifies gene fusions in RNA sequencing data
-
Placnet
-
Plasmid Constellation Network project
-
Poretools
-
toolkit for nanopore nucleotide sequencing data
-
Python3-airr
-
Data Representation Standard library for antibody and TCR sequences
-
Python3-gffutils
-
Work with GFF and GTF files in a flexible database framework
-
Python3-presto
-
toolkit for processing B and T cell sequences (Python3 module)
-
Python3-pybedtools
-
Python 3 wrapper around BEDTools for bioinformatics work
-
Python3-sqt
-
SeQuencing Tools for biological DNA/RNA high-throughput data
-
Q2cli
-
Click-based command line interface for QIIME 2
-
Qcumber
-
quality control of genomic sequences
-
Qiime
-
Quantitative Insights Into Microbial Ecology
-
Quorum
-
QUality Optimized Reads of genomic sequences
-
R-bioc-deseq2
-
R package for RNA-Seq Differential Expression Analysis
-
R-bioc-edger
-
Empirical analysis of digital gene expression data in R
-
R-bioc-hilbertvis
-
GNU R package to visualise long vector data
-
R-bioc-metagenomeseq
-
GNU R statistical analysis for sparse high-throughput sequencing
-
R-bioc-rsubread
-
Subread Sequence Alignment and Counting for R
-
R-cran-alakazam
-
Immunoglobulin Clonal Lineage and Diversity Analysis
-
R-cran-shazam
-
Immunoglobulin Somatic Hypermutation Analysis
-
R-cran-tcr
-
Advanced Data Analysis of Immune Receptor Repertoires
-
R-cran-tigger
-
Infers new Immunoglobulin alleles from Rep-Seq Data
-
Rna-star
-
ultrafast universal RNA-seq aligner
-
Rtax
-
Classification of sequence reads of 16S ribosomal RNA gene
-
Salmon
-
wicked-fast transcript quantification from RNA-seq data
-
Sambamba
-
tools for working with SAM/BAM data
-
Samblaster
-
marks duplicates, extracts discordant/split reads
-
Samtools
-
processing sequence alignments in SAM, BAM and CRAM formats
-
Scoary
-
pangenome-wide association studies
-
Scythe
-
Bayesian adaptor trimmer for sequencing reads
-
Seqprep
-
stripping adaptors and/or merging paired reads of DNA sequences with overlap
-
Seqtk
-
Fast and lightweight tool for processing sequences in the FASTA or FASTQ format
-
Sga
-
de novo genome assembler that uses string graphs
-
Sickle
-
windowed adaptive trimming tool for FASTQ files using quality
-
Smalt
-
Sequence Mapping and Alignment Tool
-
Smrtanalysis
-
software suite for single molecule, real-time sequencing
-
Snap-aligner
-
Scalable Nucleotide Alignment Program
-
Sniffles
-
structural variation caller using third-generation sequencing
-
Snp-sites
-
Binary code for the package snp-sites
-
Snpomatic
-
fast, stringent short-read mapping software
-
Soapdenovo
-
short-read assembly method to build de novo draft assembly
-
Soapdenovo2
-
short-read assembly method to build de novo draft assembly
-
Sortmerna
-
tool for filtering, mapping and OTU-picking NGS reads
-
Spades
-
genome assembler for single-cell and isolates data sets
-
Sprai
-
single-pass sequencing read accuracy improver
-
Sra-toolkit
-
utilities for the NCBI Sequence Read Archive
-
Srst2
-
Short Read Sequence Typing for Bacterial Pathogens
-
Ssake
-
genomics application for assembling millions of very short DNA sequences
-
Stacks
-
pipeline for building loci from short-read DNA sequences
-
Stringtie
-
assemble short RNAseq reads to transcripts
-
Subread
-
toolkit for processing next-gen sequencing data
-
Sumaclust
-
fast and exact clustering of genomic sequences
-
Sumatra
-
fast and exact comparison and clustering of sequences
-
Tabix
-
generic indexer for TAB-delimited genome position files
-
Transrate-tools
-
helper for transrate
-
Trimmomatic
-
flexible read trimming tool for Illumina NGS data
-
Trinityrnaseq
-
RNA-Seq De novo Assembly
-
Uc-echo
-
error correction algorithm designed for short-reads from NGS
-
Vcftools
-
Collection of tools to work with VCF files
-
Velvet
-
Nucleic acid sequence assembler for very short reads
-
Velvet-long
-
Nucleic acid sequence assembler for very short reads, long version
-
Velvetoptimiser
-
automatically optimise Velvet do novo assembly parameters
-
Vsearch
-
tool for processing metagenomic sequences
-
Wham-align
-
Wisconsin's High-Throughput Alignment Method
-
Wigeon
-
reimplementation of the Pintail 16S DNA anomaly detection utility
Official Debian packages with lower relevance
-
Nanolyse
-
remove lambda phage reads from a fastq file
-
Python3-anndata
-
annotated gene by sample numpy matrix
-
R-bioc-isoformswitchanalyzer
-
Identify, Annotate and Visualize Alternative Splicing and
Debian packages in contrib or non-free
-
Bcbio
-
toolkit for analysing high-throughput sequencing data
-
Cufflinks
-
Transcript assembly, differential expression and regulation for RNA-Seq
-
Vdjtools
-
framework for post-analysis of B/T cell repertoires
Packaging has started and developers might try the packaging code in VCS
-
Graphmap2
-
highly sensitive and accurate mapper for long, error-prone reads
-
Mosaik-aligner
-
reference-guided aligner for next-generation sequencing
-
Nanoplot
-
plotting scripts for long read sequencing data
-
R-bioc-mofa2
-
Multi-Omics Factor Analysis v2
-
Umap
-
quantify genome and methylome mappability
No known packages available
-
Annovar
-
annotate genetic variants detected from diverse genomes
-
Forge
-
genome assembler for mixed read types
This lists Debian packages related to phylogeny for use in life sciences.
The purpose of this compilation of packages is to have a handy subset of
from the med-bio metapackage which contains a lot more than only phylogeny
related software.
Official Debian packages with high relevance
-
Altree
-
program to perform phylogeny-based association and localization analysis
-
Beast-mcmc
-
Bayesian MCMC phylogenetic inference
-
Clustalw
-
global multiple nucleotide or peptide sequence alignment
-
Clustalx
-
Multiple alignment of nucleic acid and protein sequences (graphical interface)
-
Dialign
-
Segment-based multiple sequence alignment
-
Dialign-tx
-
Segment-based multiple sequence alignment
-
Exonerate
-
generic tool for pairwise sequence comparison
-
Fastdnaml
-
Tool for construction of phylogenetic trees of DNA sequences
-
Fasttree
-
phylogenetic trees from alignments of nucleotide or protein sequences
-
Figtree
-
graphical phylogenetic tree viewer
-
Gmap
-
spliced and SNP-tolerant alignment for mRNA and short reads
-
Hmmer
-
profile hidden Markov models for protein sequence analysis
-
Iqtree
-
efficient phylogenetic software by maximum likelihood
-
Jmodeltest
-
HPC selection of models of nucleotide substitution
-
Kalign
-
Global and progressive multiple sequence alignment
-
Mrbayes
-
Bayesian Inference of Phylogeny
-
Muscle
-
Multiple alignment program of protein sequences
-
Muscle3
-
multiple alignment program of protein sequences
-
Mustang
-
multiple structural alignment of proteins
-
Njplot
-
phylogenetic tree drawing program
-
Phylip
-
package of programs for inferring phylogenies
-
Phyml
-
Phylogenetic estimation using Maximum Likelihood
-
Poa
-
Partial Order Alignment for multiple sequence alignment
-
Populations
-
population genetic software
-
Pplacer
-
phylogenetic placement and downstream analysis
-
Proalign
-
Probabilistic multiple alignment program
-
Probalign
-
multiple sequence alignment using partition function posterior probabilities
-
Probcons
-
PROBabilistic CONSistency-based multiple sequence alignment
-
Proda
-
multiple alignment of protein sequences
-
Prottest
-
selection of best-fit models of protein evolution
-
Quicktree
-
Neighbor-Joining algorithm for phylogenies
-
Seaview
-
Multiplatform interface for sequence alignment and phylogeny
-
Sigma-align
-
Simple greedy multiple alignment of non-coding DNA sequences
-
Spread-phy
-
analyze and visualize phylogeographic reconstructions
-
T-coffee
-
Multiple Sequence Alignment
-
Tm-align
-
structural alignment of proteins
-
Tree-ppuzzle
-
Parallelized reconstruction of phylogenetic trees by maximum likelihood
-
Tree-puzzle
-
Reconstruction of phylogenetic trees by maximum likelihood
-
Treeview
-
Java re-implementation of Michael Eisen's TreeView
-
Treeviewx
-
Displays and prints phylogenetic trees
-
Veryfasttree
-
Speeding up the estimation of phylogenetic trees from sequences
Official Debian packages with lower relevance
-
Python3-treetime
-
inference of time stamped phylogenies and ancestral reconstruction (Python 3)
Packaging has started and developers might try the packaging code in VCS
-
Forester
-
Graphical vizualiation tool Archaeopteryx
-
Patristic
-
Calculate patristic distances and comparing the components of genetic change
No known packages available but some record of interest (WNPP bug)
-
Phylowin
-
Graphical interface for molecular phylogenetic inference
No known packages available
-
Gbioseq
-
DNA sequence editor for Linux
-
Jstreeview
-
Editor for Phylogenetic Trees
-
Phpphylotree
-
draw phylogenetic trees
-
Treetime
-
Bayesian sampling of phylogenetic trees from molecular data
This metapackage will install Debian packages related to molecular biology,
structural biology and bioinformatics for use in life sciences, that do not
depend on graphical toolkits and therefore can fit on system images for use
in cloud computing clusters, where space can be limited.
Official Debian packages with high relevance
-
Abyss
-
de novo, parallel, sequence assembler for short reads
-
Acedb-other
-
retrieval of DNA or protein sequences
-
Aevol
-
digital genetics model to run Evolution Experiments in silico
-
Alien-hunter
-
Interpolated Variable Order Motifs to identify horizontally acquired DNA
-
Altree
-
program to perform phylogeny-based association and localization analysis
-
Amap-align
-
Protein multiple alignment by sequence annealing
-
Ampliconnoise
-
removal of noise from 454 sequenced PCR amplicons
-
Anfo
-
Short Read Aligner/Mapper from MPG
-
Aragorn
-
tRNA and tmRNA detection in nucleotide sequences
-
Arden
-
specificity control for read alignments using an artificial reference
-
Autodock
-
analysis of ligand binding to protein structure
-
Autodock-vina
-
docking of small molecules to proteins
-
Autogrid
-
pre-calculate binding of ligands to their receptor
-
Bamtools
-
toolkit for manipulating BAM (genome alignment) files
-
Bedtools
-
suite of utilities for comparing genomic features
-
Bioperl
-
Perl tools for computational molecular biology
-
Bioperl-run
-
BioPerl wrappers: scripts
-
Biosquid
-
utilities for biological sequence analysis
-
Blast2
-
transitional dummy package to ncbi-blast+-legacy
-
Bowtie
-
Ultrafast memory-efficient short read aligner
-
Bowtie2
-
ultrafast memory-efficient short read aligner
-
Boxshade
-
Pretty-printing of multiple sequence alignments
-
Bwa
-
Burrows-Wheeler Aligner
-
Cassiopee
-
index and search tool in genomic sequences
-
Cd-hit
-
suite of programs designed to quickly group sequences
-
Cdbfasta
-
Constant DataBase indexing and retrieval tools for multi-FASTA files
-
Circos
-
plotter for visualizing data
-
Clearcut
-
extremely efficient phylogenetic tree reconstruction
-
Clonalframe
-
inference of bacterial microevolution using multilocus sequence data
-
Clustalo
-
General-purpose multiple sequence alignment program for proteins
-
Clustalw
-
global multiple nucleotide or peptide sequence alignment
-
Concavity
-
predictor of protein ligand binding sites from structure and conservation
-
Conservation-code
-
protein sequence conservation scoring tool
-
Datamash
-
statistics tool for command-line interface
-
Dialign
-
Segment-based multiple sequence alignment
-
Dialign-tx
-
Segment-based multiple sequence alignment
-
Discosnp
-
discovering Single Nucleotide Polymorphism from raw set(s) of reads
-
Disulfinder
-
cysteines disulfide bonding state and connectivity predictor
-
Dnaclust
-
tool for clustering millions of short DNA sequences
-
Dssp
-
protein secondary structure assignment based on 3D structure
-
Embassy-domainatrix
-
Extra EMBOSS commands to handle domain classification file
-
Embassy-domalign
-
Extra EMBOSS commands for protein domain alignment
-
Embassy-domsearch
-
Extra EMBOSS commands to search for protein domains
-
Emboss
-
European molecular biology open software suite
-
Exonerate
-
generic tool for pairwise sequence comparison
-
Fastdnaml
-
Tool for construction of phylogenetic trees of DNA sequences
-
Fastlink
-
faster version of pedigree programs of Linkage
-
Fastqc
-
quality control for high throughput sequence data
-
Fasttree
-
phylogenetic trees from alignments of nucleotide or protein sequences
-
Fitgcp
-
fitting genome coverage distributions with mixture models
-
Flexbar
-
flexible barcode and adapter removal for sequencing platforms
-
Freecontact
-
fast protein contact predictor
-
Gasic
-
genome abundance similarity correction
-
Genometools
-
versatile genome analysis toolkit
-
Gff2aplot
-
pair-wise alignment-plots for genomic sequences in PostScript
-
Gff2ps
-
produces PostScript graphical output from GFF-files
-
Giira
-
RNA-Seq driven gene finding incorporating ambiguous reads
-
Glam2
-
gapped protein motifs from unaligned sequences
-
Gmap
-
spliced and SNP-tolerant alignment for mRNA and short reads
-
Grinder
-
Versatile omics shotgun and amplicon sequencing read simulator
-
Gromacs
-
Molecular dynamics simulator, with building and analysis tools
-
Hhsuite
-
sensitive protein sequence searching based on HMM-HMM alignment
-
Hisat2
-
graph-based alignment of short nucleotide reads to many genomes
-
Hmmer
-
profile hidden Markov models for protein sequence analysis
-
Idba
-
iterative De Bruijn Graph short read assemblers
-
Infernal
-
inference of RNA secondary structural alignments
-
Jellyfish
-
count k-mers in DNA sequences
-
Kalign
-
Global and progressive multiple sequence alignment
-
Kissplice
-
Detection of various kinds of polymorphisms in RNA-seq data
-
Last-align
-
genome-scale comparison of biological sequences
-
Loki
-
MCMC linkage analysis on general pedigrees
-
Macs
-
Model-based Analysis of ChIP-Seq on short reads sequencers
-
Mafft
-
Multiple alignment program for amino acid or nucleotide sequences
-
Mapsembler2
-
bioinformatics targeted assembly software
-
Maq
-
maps short fixed-length polymorphic DNA sequence reads to reference sequences
-
Melting
-
compute the melting temperature of nucleic acid duplex
-
Minia
-
short-read biological sequence assembler
-
Mipe
-
Tools to store PCR-derived data
-
Mira-assembler
-
Whole Genome Shotgun and EST Sequence Assembler
-
Mlv-smile
-
Find statistically significant patterns in sequences
-
Mothur
-
sequence analysis suite for research on microbiota
-
Mrbayes
-
Bayesian Inference of Phylogeny
-
Mummer
-
Efficient sequence alignment of full genomes
-
Muscle
-
Multiple alignment program of protein sequences
-
Muscle3
-
multiple alignment program of protein sequences
-
Mustang
-
multiple structural alignment of proteins
-
Ncbi-epcr
-
Tool to test a DNA sequence for the presence of sequence tagged sites
-
Ncbi-tools-bin
-
NCBI libraries for biology applications (text-based utilities)
-
Ncoils
-
coiled coil secondary structure prediction
-
Neobio
-
computes alignments of amino acid and nucleotide sequences
-
Paraclu
-
Parametric clustering of genomic and transcriptomic features
-
Parsinsert
-
Parsimonious Insertion of unclassified sequences into phylogenetic trees
-
Pdb2pqr
-
Preparation of protein structures for electrostatics calculations
-
Perm
-
efficient mapping of short reads with periodic spaced seeds
-
Phyml
-
Phylogenetic estimation using Maximum Likelihood
-
Phyutility
-
simple analyses or modifications on both phylogenetic trees and data matrices
-
Picard-tools
-
Command line tools to manipulate SAM and BAM files
-
Plink
-
whole-genome association analysis toolset
-
Plink1.9
-
whole-genome association analysis toolset
-
Plink2
-
whole-genome association analysis toolset
-
Poa
-
Partial Order Alignment for multiple sequence alignment
-
Prank
-
Probabilistic Alignment Kit for DNA, codon and amino-acid sequences
-
Prime-phylo
-
bayesian estimation of gene trees taking the species tree into account
-
Primer3
-
tool to design flanking oligo nucleotides for DNA amplification
-
Probabel
-
Toolset for Genome-Wide Association Analysis
-
Probcons
-
PROBabilistic CONSistency-based multiple sequence alignment
-
Proda
-
multiple alignment of protein sequences
-
Prodigal
-
Microbial (bacterial and archaeal) gene finding program
-
Python3-biomaj3-cli
-
BioMAJ client
-
Python3-biopython
-
Python3 library for bioinformatics
-
Python3-cogent3
-
framework for genomic biology
-
Qiime
-
Quantitative Insights Into Microbial Ecology
-
R-bioc-edger
-
Empirical analysis of digital gene expression data in R
-
R-bioc-hilbertvis
-
GNU R package to visualise long vector data
-
R-cran-pvclust
-
Hierarchical Clustering with P-Values via Multiscale Bootstrap
-
R-cran-qtl
-
GNU R package for genetic marker linkage analysis
-
R-cran-vegan
-
Community Ecology Package for R
-
R-other-mott-happy.hbrem
-
GNU R package for fine-mapping complex diseases
-
Raster3d
-
tools for generating images of proteins or other molecules
-
Readseq
-
Conversion between sequence formats
-
Rnahybrid
-
Fast and effective prediction of microRNA/target duplexes
-
Rtax
-
Classification of sequence reads of 16S ribosomal RNA gene
-
Samtools
-
processing sequence alignments in SAM, BAM and CRAM formats
-
Seqan-apps
-
C++ library for the analysis of biological sequences
-
Sibsim4
-
align expressed RNA sequences on a DNA template
-
Sigma-align
-
Simple greedy multiple alignment of non-coding DNA sequences
-
Sim4
-
tool for aligning cDNA and genomic DNA
-
Smalt
-
Sequence Mapping and Alignment Tool
-
Snap
-
location of genes from DNA sequence with hidden markov model
-
Soapdenovo
-
short-read assembly method to build de novo draft assembly
-
Soapdenovo2
-
short-read assembly method to build de novo draft assembly
-
Sra-toolkit
-
utilities for the NCBI Sequence Read Archive
-
Ssake
-
genomics application for assembling millions of very short DNA sequences
-
Staden-io-lib-utils
-
programs for manipulating DNA sequencing files
-
T-coffee
-
Multiple Sequence Alignment
-
Tabix
-
generic indexer for TAB-delimited genome position files
-
Theseus
-
superimpose macromolecules using maximum likelihood
-
Tigr-glimmer
-
Gene detection in archea and bacteria
-
Tree-ppuzzle
-
Parallelized reconstruction of phylogenetic trees by maximum likelihood
-
Tree-puzzle
-
Reconstruction of phylogenetic trees by maximum likelihood
-
Vcftools
-
Collection of tools to work with VCF files
-
Velvet
-
Nucleic acid sequence assembler for very short reads
-
Veryfasttree
-
Speeding up the estimation of phylogenetic trees from sequences
-
Wise
-
comparison of biopolymers, like DNA and protein sequences
Debian packages in contrib or non-free
-
Cufflinks
-
Transcript assembly, differential expression and regulation for RNA-Seq
-
Embassy-phylip
-
EMBOSS conversions of the programs in the phylip package
Packaging has started and developers might try the packaging code in VCS
-
Bagpipe
-
genomewide LD mapping
Here you can find software that is useful to build a
content management system for medical care.
Packaging has started and developers might try the packaging code in VCS
-
Xnat
-
platform for data management and productivity tasks in neuroimaging
-
Zope-zms
-
Content management for science, technology and medicine
No known packages available
-
Hid
-
database management system for clinical imaging
The Debian Med team intends to take part at the
COVID-19 Biohackathon (April 5-11, 2020)
This task was created only for the purpose to list relevant packages.
Official Debian packages with high relevance
-
Abacas
-
close gaps in genomic alignments from short reads
-
Abyss
-
de novo, parallel, sequence assembler for short reads
-
Allelecount
-
NGS copy number algorithms
-
Assembly-stats
-
get assembly statistics from FASTA and FASTQ files
-
Augur
-
pipeline components for real-time virus analysis
-
Bamclipper
-
Remove gene-specific primer sequences from SAM/BAM alignments
-
Bamkit
-
tools for common BAM file manipulations
-
Bbmap
-
BBTools genomic aligner and other tools for short sequences
-
Bcalm
-
de Bruijn compaction in low memory
-
Bcftools
-
genomic variant calling and manipulation of VCF/BCF files
-
Bedtools
-
suite of utilities for comparing genomic features
-
Biobambam2
-
tools for early stage alignment file processing
-
Bowtie2
-
ultrafast memory-efficient short read aligner
-
Busco
-
benchmarking sets of universal single-copy orthologs
-
Bustools
-
program for manipulating BUS files for single cell RNA-Seq datasets
-
Bwa
-
Burrows-Wheeler Aligner
-
Cat-bat
-
taxonomic classification of contigs and metagenome-assembled genomes (MAGs)
-
Centrifuge
-
rapid and memory-efficient system for classification of DNA sequences
-
Changeo
-
Repertoire clonal assignment toolkit (Python 3)
-
Chip-seq
-
tools performing common ChIP-Seq data analysis tasks
-
Clonalframeml
-
Efficient Inference of Recombination in Whole Bacterial Genomes
-
Cutadapt
-
Clean biological sequences from high-throughput sequencing reads
-
Cwltool
-
Common Workflow Language reference implementation
-
Dcmtk
-
OFFIS DICOM toolkit command line utilities
-
Delly
-
Structural variant discovery by read analysis
-
Dextractor
-
(d)extractor and compression command library
-
Diamond-aligner
-
accelerated BLAST compatible local sequence aligner
-
Discosnp
-
discovering Single Nucleotide Polymorphism from raw set(s) of reads
-
Drop-seq-tools
-
analyzing Drop-seq data
-
Fasta3
-
tools for searching collections of biological sequences
-
Fastani
-
Fast alignment-free computation of whole-genome Average Nucleotide Identity
-
Fastp
-
Ultra-fast all-in-one FASTQ preprocessor
-
Fastqc
-
quality control for high throughput sequence data
-
Filtlong
-
quality filtering tool for long reads of genome sequences
-
Flash
-
Fast Length Adjustment of SHort reads
-
Flye
-
de novo assembler for single molecule sequencing reads using repeat graphs
-
Freebayes
-
Bayesian haplotype-based polymorphism discovery and genotyping
-
Genometools
-
versatile genome analysis toolkit
-
Gffread
-
GFF/GTF format conversions, region filtering, FASTA sequence extraction
-
Ginkgocadx
-
Medical Imaging Software and complete DICOM Viewer
-
Gnumed-client
-
medical practice management - Client
-
Gnumed-server
-
medical practice management - server
-
Gromacs
-
Molecular dynamics simulator, with building and analysis tools
-
Gubbins
-
phylogenetic analysis of genome sequences
-
Imagej
-
Image processing program with a focus on microscopy images
-
Ivar
-
functions broadly useful for viral amplicon-based sequencing
-
Kalign
-
Global and progressive multiple sequence alignment
-
Kallisto
-
near-optimal RNA-Seq quantification
-
Kraken2
-
taxonomic classification system using exact k-mer matches
-
Lastz
-
pairwise aligning DNA sequences
-
Libbbhash-dev
-
bloom-filter based minimal perfect hash function library
-
Libchipcard-dev
-
API for smartcard readers
-
Libgclib-dev
-
header files for Genome Code Lib (GCLib)
-
Libgdcm-tools
-
Grassroots DICOM tools and utilities
-
Libhtscodecs-dev
-
Development headers for custom compression for CRAM and others
-
Libics-dev
-
Image Cytometry Standard file reading and writing (devel)
-
Libmaus2-dev
-
collection of data structures and algorithms for biobambam (devel)
-
Libmilib-java
-
library for Next Generation Sequencing (NGS) data processing
-
Libseqan3-dev
-
C++ library for the analysis of biological sequences v3 (development)
-
Lighter
-
fast and memory-efficient sequencing error corrector
-
Lumpy-sv
-
general probabilistic framework for structural variant discovery
-
Mecat2
-
ultra-fast and accurate de novo assembly tools for SMRT reads
-
Megahit
-
ultra-fast and memory-efficient meta-genome assembler
-
Metabat
-
robust statistical framework for reconstructing genomes from metagenomic data
-
Minia
-
short-read biological sequence assembler
-
Minimap2
-
versatile pairwise aligner for genomic and spliced nucleotide sequences
-
Mmb
-
model the structure and dynamics of macromolecules
-
Mmseqs2
-
ultra fast and sensitive protein search and clustering
-
Multiqc
-
output integration for RNA sequencing across tools and samples
-
Muscle
-
Multiple alignment program of protein sequences
-
Muscle3
-
multiple alignment program of protein sequences
-
Nanofilt
-
filtering and trimming of long read sequencing data
-
Nanolyse
-
remove lambda phage reads from a fastq file
-
Nanook
-
pre- and post-alignment analysis of nanopore sequencing data
-
Nanopolish
-
consensus caller for nanopore sequencing data
-
Nanosv
-
structural variant caller for nanopore data
-
Ncbi-blast+
-
next generation suite of BLAST sequence search tools
-
Ngmlr
-
CoNvex Gap-cost alignMents for Long Reads
-
Nthash
-
Methods to evaluate runtime and uniformity tests for hashing methods
-
Odil
-
C++11 library for the DICOM standard (application)
-
Orthanc
-
Lightweight, RESTful DICOM server for medical imaging
-
Orthanc-dicomweb
-
Plugin to extend Orthanc with support of WADO and DICOMweb
-
Orthanc-python
-
Develop plugins for Orthanc using the Python programming language
-
Orthanc-wsi
-
Whole-slide imaging support for Orthanc (digital pathology)
-
Paleomix
-
pipelines and tools for the processing of ancient and modern HTS data
-
Parallel-fastq-dump
-
parallel fastq-dump wrapper
-
Parasail
-
Aligner based on libparasail
-
Picard-tools
-
Command line tools to manipulate SAM and BAM files
-
Picopore
-
lossless compression of Nanopore files
-
Pigx-rnaseq
-
pipeline for checkpointed and distributed RNA-seq analyses
-
Pinfish
-
Collection of tools to annotate genomes using long read transcriptomics data
-
Plasmidid
-
mapping-based, assembly-assisted plasmid identification tool
-
Plink1.9
-
whole-genome association analysis toolset
-
Plink2
-
whole-genome association analysis toolset
-
Plip
-
fully automated protein-ligand interaction profiler
-
Porechop
-
adapter trimmer for Oxford Nanopore reads
-
Poretools
-
toolkit for nanopore nucleotide sequencing data
-
Pplacer
-
phylogenetic placement and downstream analysis
-
Presto
-
toolkit for processing B and T cell sequences
-
Prinseq-lite
-
PReprocessing and INformation of SEQuence data (lite version)
-
Prokka
-
rapid annotation of prokaryotic genomes
-
Proteinortho
-
Detection of (Co-)orthologs in large-scale protein analysis
-
Pybedtools-bin
-
Scripts produced for pybedtools
-
Pycoqc
-
computes metrics and generates Interactive QC plots
-
Python3-biom-format
-
Biological Observation Matrix (BIOM) format (Python 3)
-
Python3-biopython
-
Python3 library for bioinformatics
-
Python3-bx
-
library to manage genomic data and its alignment
-
Python3-cgecore
-
Python3 module for the Center for Genomic Epidemiology
-
Python3-cogent3
-
framework for genomic biology
-
Python3-cooler
-
library for a sparse, compressed, binary persistent storage
-
Python3-cyvcf2
-
VCF parser based on htslib (Python 3)
-
Python3-depinfo
-
retrieve and print Python 3 package dependencies
-
Python3-drmaa
-
interface to DRMAA-compliant distributed resource management systems
-
Python3-etelemetry
-
lightweight Python3 client to communicate with the etelemetry server
-
Python3-gffutils
-
Work with GFF and GTF files in a flexible database framework
-
Python3-htseq
-
Python3 high-throughput genome sequencing read analysis utilities
-
Python3-nanoget
-
extract information from Oxford Nanopore sequencing data and alignments
-
Python3-nanomath
-
simple math function for other Oxford Nanopore processing scripts
-
Python3-pairix
-
1D/2D indexing and querying with a pair of genomic coordinates
-
Python3-pairtools
-
Framework to process sequencing data from a Hi-C experiment
-
Python3-pauvre
-
QC and genome browser plotting Oxford Nanopore and PacBio long reads
-
Python3-pbcommand
-
common command-line interface for Pacific Biosciences analysis modules
-
Python3-pbcore
-
Python 3 library for processing PacBio data files
-
Python3-pyani
-
Python3 module for average nucleotide identity analyses
-
Python3-pychopper
-
identify, orient and trim full-length Nanopore cDNA reads
-
Python3-pydicom
-
DICOM medical file reading and writing (Python 3)
-
Python3-pyfaidx
-
efficient random access to fasta subsequences for Python 3
-
Python3-pynn
-
simulator-independent specification of neuronal network models
-
Python3-pysam
-
interface for the SAM/BAM sequence alignment and mapping format (Python 3)
-
Python3-questplus
-
QUEST+ implementation in Python3
-
Python3-scitrack
-
Python3 library to track scientific data
-
Python3-screed
-
short nucleotide read sequence utils in Python 3
-
Python3-seirsplus
-
Models of SEIRS epidemic dynamics with extensions
-
Python3-streamz
-
build pipelines to manage continuous streams of data
-
Python3-tinyalign
-
numerical representation of differences between strings
-
Python3-toolz
-
List processing tools and functional utilities
-
Python3-torch
-
Tensors and Dynamic neural networks in Python (Python Interface)
-
Python3-tornado
-
scalable, non-blocking web server and tools - Python 3 package
-
Python3-treetime
-
inference of time stamped phylogenies and ancestral reconstruction (Python 3)
-
Python3-vcf
-
Variant Call Format (VCF) parser for Python 3
-
Q2-cutadapt
-
QIIME 2 plugin to work with adapters in sequence data
-
Q2-feature-table
-
QIIME 2 plugin supporting operations on feature tables
-
Q2-quality-filter
-
QIIME2 plugin for PHRED-based filtering and trimming
-
Qcat
-
demultiplexing Oxford Nanopore reads from FASTQ files
-
Quicktree
-
Neighbor-Joining algorithm for phylogenies
-
R-bioc-htsfilter
-
GNU R filter replicated high-throughput transcriptome sequencing data
-
R-bioc-limma
-
linear models for microarray data
-
R-bioc-mutationalpatterns
-
GNU R comprehensive genome-wide analysis of mutational processes
-
R-bioc-pwmenrich
-
PWM enrichment analysis
-
R-bioc-rcpi
-
molecular informatics toolkit for compound-protein interaction
-
R-bioc-rgsepd
-
GNU R gene set enrichment / projection displays
-
R-bioc-rsamtools
-
GNU R binary alignment (BAM), variant call (BCF), or tabix file import
-
R-bioc-tcgabiolinks
-
GNU R/Bioconductor package for integrative analysis with GDC data
-
R-cran-alakazam
-
Immunoglobulin Clonal Lineage and Diversity Analysis
-
R-cran-covid19us
-
cases of COVID-19 in the United States prepared for GNU R
-
R-cran-diagnosismed
-
medical diagnostic test accuracy analysis toolkit
-
R-cran-epi
-
GNU R epidemiological analysis
-
R-cran-epibasix
-
GNU R Elementary Epidemiological Functions
-
R-cran-epicalc
-
GNU R Epidemiological calculator
-
R-cran-epiestim
-
GNU R estimate time varying reproduction numbers from rpidemic curves
-
R-cran-epir
-
GNU R Functions for analysing epidemiological data
-
R-cran-epitools
-
GNU R Epidemiology Tools for Data and Graphics
-
R-cran-hms
-
GNU R pretty time of day
-
R-cran-incidence
-
GNU R compute, handle, plot and model incidence of dated events
-
R-cran-kernelheaping
-
GNU R kernel density estimation for heaped and rounded data
-
R-cran-lexrankr
-
extractive summarization of text with the LexRank algorithm
-
R-cran-mediana
-
clinical trial simulations
-
R-cran-msm
-
GNU R Multi-state Markov and hidden Markov models in continuous time
-
R-cran-qtl
-
GNU R package for genetic marker linkage analysis
-
R-cran-seroincidence
-
GNU R seroincidence calculator tool
-
R-cran-sf
-
Simple Features for R
-
R-cran-shazam
-
Immunoglobulin Somatic Hypermutation Analysis
-
R-cran-sjplot
-
GNU R data visualization for statistics in social science
-
R-cran-spp
-
GNU R ChIP-seq processing pipeline
-
R-cran-stringi
-
GNU R character string processing facilities
-
R-cran-surveillance
-
GNU R package for the Modeling and Monitoring of Epidemic Phenomena
-
R-cran-tigger
-
Infers new Immunoglobulin alleles from Rep-Seq Data
-
R-other-ascat
-
Allele-Specific Copy Number Analysis of Tumours
-
Ragout
-
Reference-Assisted Genome Ordering UTility
-
Readucks
-
Nanopore read de-multiplexer (read demux -> readux -> readucks, innit)
-
Recan
-
genetic distance plotting for recombination events analysis
-
Rna-star
-
ultrafast universal RNA-seq aligner
-
Rsem
-
RNA-Seq by Expectation-Maximization
-
Ruby-bio
-
Ruby tools for computational molecular biology
-
Salmon
-
wicked-fast transcript quantification from RNA-seq data
-
Samblaster
-
marks duplicates, extracts discordant/split reads
-
Samclip
-
filter SAM file for soft and hard clipped alignments
-
Samtools
-
processing sequence alignments in SAM, BAM and CRAM formats
-
Scrappie
-
basecaller for Nanopore sequencer
-
Sepp
-
phylogeny with ensembles of Hidden Markov Models
-
Seqkit
-
cross-platform and ultrafast toolkit for FASTA/Q file manipulation
-
Seqmagick
-
imagemagick-like frontend to Biopython SeqIO
-
Shapeit4
-
fast and accurate method for estimation of haplotypes (phasing)
-
Shiny-server
-
put Shiny web apps online
-
Shovill
-
Assemble bacterial isolate genomes from Illumina paired-end reads
-
Smrtanalysis
-
software suite for single molecule, real-time sequencing
-
Snakemake
-
pythonic workflow management system
-
Snpeff
-
genetic variant annotation and effect prediction toolbox - tool
-
Snpsift
-
tool to annotate and manipulate genome variants - tool
-
Spades
-
genome assembler for single-cell and isolates data sets
-
Spaln
-
splicing-aware transcript-alignment to genomic DNA
-
Staden-io-lib-utils
-
programs for manipulating DNA sequencing files
-
Stringtie
-
assemble short RNAseq reads to transcripts
-
Sumaclust
-
fast and exact clustering of genomic sequences
-
Texlive-science
-
??? missing short description for package texlive-science :-(
-
Thesias
-
Testing Haplotype Effects In Association Studies
-
Tiddit
-
structural variant calling
-
Tipp
-
tool for Taxonomic Identification and Phylogenetic Profiling
-
Tnseq-transit
-
statistical calculations of essentiality of genes or genomic regions
-
Toil
-
cross-platform workflow engine
-
Tombo
-
identification of modified nucleotides from raw nanopore sequencing data
-
Tophat-recondition
-
post-processor for TopHat unmapped reads
-
Trinculo
-
toolkit to carry out genetic association for multi-category phenotypes
-
Umap-learn
-
Uniform Manifold Approximation and Projection
-
Umis
-
tools for processing UMI RNA-tag data
-
Uncalled
-
Utility for Nanopore Current Alignment to Large Expanses of DNA
-
Unicycler
-
hybrid assembly pipeline for bacterial genomes
-
Vg
-
tools for working with genome variation graphs
-
Vsearch
-
tool for processing metagenomic sequences
-
Vt
-
toolset for short variant discovery in genetic sequence data
-
Workrave
-
Repetitive Strain Injury prevention tool
-
Wtdbg2
-
de novo sequence assembler for long noisy reads
-
Yanagiba
-
filter low quality Oxford Nanopore reads basecalled with Albacore
-
Yanosim
-
read simulator nanopore DRS datasets
Official Debian packages with lower relevance
-
Libsimde-dev
-
Implementations of SIMD instructions for all systems
-
Python3-anndata
-
annotated gene by sample numpy matrix
-
Python3-mmtf
-
binary encoding of biological structures (Python 3)
-
R-bioc-rsubread
-
Subread Sequence Alignment and Counting for R
Debian packages in contrib or non-free
-
Bcbio
-
toolkit for analysing high-throughput sequencing data
-
Python3-seqcluster
-
analysis of small RNA in NGS data
-
Varscan
-
variant detection in next-generation sequencing data
-
Vienna-rna
-
RNA sequence analysis
Debian packages in experimental
-
Libtensorflow-framework2
-
Computation using data flow graphs for scalable machine learning
Packaging has started and developers might try the packaging code in VCS
-
Arvados
-
managing and analyzing biomedical big data
-
Auspice
-
web app for visualizing pathogen evolution
-
Blat
-
BLAST-Like Alignment Tool
-
Chime
-
COVID-19 Hospital Impact Model for Epidemics
-
Covpipe
-
pipeline to generate consensus sequences from NGS reads
-
Ensembl-vep
-
Variant Effect Predictor predicting the functional effects of genomic variants
-
Fieldbioinformatics
-
pipeline with virus identification with Nanopore sequencer
-
Flappie
-
flip-flop basecaller for Oxford Nanopore reads
-
Graphmap2
-
highly sensitive and accurate mapper for long, error-prone reads
-
Manta
-
structural variant and indel caller for mapped sequencing data
-
Medaka
-
sequence correction provided by ONT Research
-
Nanoplot
-
plotting scripts for long read sequencing data
-
Ncbi-magicblast
-
RNA-seq mapping tool
-
Nextflow
-
DSL for data-driven computational pipelines
-
Nextstrain-ncov
-
Nextstrain build for novel coronavirus (nCoV)
-
Nf-core-artic
-
nf-core ARTIC field bioinformatics viral genome pipeline
-
Oncofuse
-
predicting oncogenic potential of gene fusions
-
Optitype
-
precision HLA typing from next-generation sequencing data
-
Pangolin
-
Phylogenetic Assignment of Named Global Outbreak LINeages
-
Pomoxis
-
analysis components from Oxford Nanopore Research
-
Python3-idseq-dag
-
Pipeline engine for IDseq (Python 3)
-
Python3-scanpy
-
Single-Cell Analysis in Python
-
Qualimap
-
evaluating next generation sequencing alignment data
-
Quast
-
Quality Assessment Tool for Genome Assemblies
-
R-cran-covid19
-
GNU R Coronavirus COVID-19 data acquisition and visualization
-
R-other-fastbaps
-
A fast genetic clustering algorithm that approximates a Dirichlet Process Mixture model
-
Rosa
-
Removal of Spurious Antisense in biological RNA sequences
-
Sailfish
-
RNA-seq expression estimation
-
Seqwish
-
alignment to variation graph inducer
-
Signalalign
-
HMM-HDP models for MinION signal alignments
-
Streamlit
-
fast way to build custom ML tools
-
Strelka
-
strelka2 germline and somatic small variant caller
-
Ufasta
-
utility to manipulate fasta files
-
Vadr
-
classification and annotation of viral sequences
This metapackage will install free drug databases and related
applications. The database can be accessed by any EMR using
the application.
Official Debian packages with high relevance
-
Freediams
-
pharmaceutical drug prescription and interaction manager
-
Freemedforms-freedata
-
free extra-data for the FreeMedForms project
-
Python3-hl7
-
Python3 library for parsing HL7 messages
Official Debian packages with lower relevance
-
Oscar
-
Open Source CPAP Analysis Reporter (OSCAR)
No known packages available
-
Drugref.org
-
pharmaceutical reference database
This metapackage contains dependencies for a collection of software
which might be helpful for dentists to manage their practice.
Official Debian packages with high relevance
-
Entangle
-
Tethered Camera Control & Capture
-
Imagetooth
-
library generating images of teeth for odontograms
This metapackage will install tools that are useful in epidemiological
research. Several packages making use of the GNU R data language for
statistical investigation. It might be a good idea to read the paper
"A short introduction to R for Epidemiology" at
http://staff.pubhealth.ku.dk/%7Ebxc/Epi/R-intro.pdf
Official Debian packages with high relevance
-
Python3-seirsplus
-
Models of SEIRS epidemic dynamics with extensions
-
Python3-torch
-
Tensors and Dynamic neural networks in Python (Python Interface)
-
Python3-treetime
-
inference of time stamped phylogenies and ancestral reconstruction (Python 3)
-
R-cran-covid19us
-
cases of COVID-19 in the United States prepared for GNU R
-
R-cran-diagnosismed
-
medical diagnostic test accuracy analysis toolkit
-
R-cran-epi
-
GNU R epidemiological analysis
-
R-cran-epibasix
-
GNU R Elementary Epidemiological Functions
-
R-cran-epicalc
-
GNU R Epidemiological calculator
-
R-cran-epiestim
-
GNU R estimate time varying reproduction numbers from rpidemic curves
-
R-cran-epir
-
GNU R Functions for analysing epidemiological data
-
R-cran-epitools
-
GNU R Epidemiology Tools for Data and Graphics
-
R-cran-incidence
-
GNU R compute, handle, plot and model incidence of dated events
-
R-cran-kernelheaping
-
GNU R kernel density estimation for heaped and rounded data
-
R-cran-lexrankr
-
extractive summarization of text with the LexRank algorithm
-
R-cran-prevalence
-
GNU R tools for prevalence assessment studies
-
R-cran-seroincidence
-
GNU R seroincidence calculator tool
-
R-cran-sf
-
Simple Features for R
-
R-cran-sjplot
-
GNU R data visualization for statistics in social science
-
R-cran-surveillance
-
GNU R package for the Modeling and Monitoring of Epidemic Phenomena
Official Debian packages with lower relevance
-
Python3-epimodels
-
simple interface to simulate mathematical epidemic models in Python3
-
R-cran-cmprsk
-
GNU R subdistribution analysis of competing risks
-
R-cran-msm
-
GNU R Multi-state Markov and hidden Markov models in continuous time
-
Shiny-server
-
put Shiny web apps online
Packaging has started and developers might try the packaging code in VCS
-
Chime
-
COVID-19 Hospital Impact Model for Epidemics
-
Epifire
-
model the spread of an infectious disease in a population
-
Netepi-analysis
-
network-enabled tools for epidemiology and public health practice
-
Netepi-collection
-
network-enabled tools for epidemiology and public health practice
-
R-cran-covid19
-
GNU R Coronavirus COVID-19 data acquisition and visualization
-
Ushahidi
-
web platform for information collection
No known packages available but some record of interest (WNPP bug)
-
Repast
-
framework for creating agent based simulations
This metapackage contains dependencies for software and that could
be useful ro run a Hospital Information System. While there is
continuous work going on to package a ready to install system currently
only preconditions are finished but hopefully helpful in hospitals
anyway.
Official Debian packages with high relevance
-
Fis-gtm
-
metapackage for the latest version of FIS-GT.M database
-
Orthanc-wsi
-
Whole-slide imaging support for Orthanc (digital pathology)
Packaging has started and developers might try the packaging code in VCS
-
Care2x
-
integrated hospital information system
-
Openmrs
-
enterprise electronic medical record system framework
-
Tryton-modules-health
-
Tryton Application Platform (Health Module)
-
Vista-foia
-
metapackage for the latest version of vista-foia.
Unofficial packages built by somebody else
-
Oscar-mcmaster
-
Oscar (Web) A medical web application for electronic medical records
No known packages available but some record of interest (WNPP bug)
-
World-vista
-
repackage and extended version of VistA produced by WorldVistA
No known packages available
-
Hkma-cms
-
clinic management system
-
Ipath
-
telemedicine platform
-
Openeyes
-
ophthalmology electronic patient record system
-
Openmaxims
-
patient administration system and electronic patient record
-
Patientos
-
Healthcare Information System (HIS) for small hospitals and clinics
This metapackage will install Debian packages which might be useful in
medical image processing and visualization.
On one hand, it installs several packages supporting various image file
formats and image management, like DICOM (Digital Imaging and
Communications in Medicine) which is the de-facto standard for medical
image management, and NIFTI. On the other hand, it provides a variety of
software packages that can be used for visualization and for image processing
- either from a graphical user interface, the command line, or implemented in
workflows.
Official Debian packages with high relevance
-
Amide
-
software for Medical Imaging
-
Ants
-
advanced normalization tools for brain and image analysis
-
Bart
-
tools for computational magnetic resonance imaging
-
Bart-view
-
viewer for multi-dimensional complex-valued data
-
Biosig-tools
-
format conversion tools for biomedical data formats
-
Camitk-imp
-
workbench application for the CamiTK library
-
Caret
-
??? missing short description for package caret :-(
-
Ctn
-
Central Test Node, a DICOM implementation for medical imaging
-
Ctsim
-
Computed tomography simulator
-
Dcm2niix
-
next generation DICOM to NIfTI converter
-
Dcmtk
-
OFFIS DICOM toolkit command line utilities
-
Dicom3tools
-
DICOM medical image files manipulation and conversion tools
-
Dicomscope
-
OFFIS DICOM Viewer
-
Fslview
-
??? missing short description for package fslview :-(
-
Gdf-tools
-
IO library for the GDF -- helper tools
-
Ginkgocadx
-
Medical Imaging Software and complete DICOM Viewer
-
Gwyddion
-
Scanning Probe Microscopy visualization and analysis tool
-
Heudiconv
-
DICOM converter with support for structure heuristics
-
Imagej
-
Image processing program with a focus on microscopy images
-
Imagevis3d
-
desktop volume rendering application for large data
-
Invesalius
-
3D medical imaging reconstruction software
-
Ismrmrd-tools
-
command-line tools for ISMRMRD
-
Itksnap
-
semi-automatic segmentation of structures in 3D images
-
King
-
interactive system for three-dimensional vector graphics
-
Libgdcm-tools
-
Grassroots DICOM tools and utilities
-
Medcon
-
Medical Image (DICOM, ECAT, ...) conversion tool
-
Mia-tools
-
Command line tools for gray scale image processing
-
Mia-viewit
-
??? missing short description for package mia-viewit :-(
-
Mialmpick
-
Tools for landmark picking in 3D volume data sets
-
Minc-tools
-
MNI medical image format tools
-
Mricron
-
magnetic resonance image conversion, viewing and analysis
-
Mrtrix3
-
diffusion-weighted MRI white matter tractography
-
Nifti-bin
-
tools shipped with the NIfTI library
-
Odil
-
C++11 library for the DICOM standard (application)
-
Odin
-
develop, simulate and run magnetic resonance sequences
-
Openslide-tools
-
Manipulation and conversion tools for OpenSlide
-
Orthanc
-
Lightweight, RESTful DICOM server for medical imaging
-
Orthanc-wsi
-
Whole-slide imaging support for Orthanc (digital pathology)
-
Pixelmed-apps
-
DICOM implementation containing Image Viewer and a ECG Viewer - cli
-
Plastimatch
-
medical image reconstruction and registration
-
Python3-dipy
-
Python library for the analysis of diffusion MRI datasets
-
Python3-nibabel
-
Python3 bindings to various neuroimaging data formats
-
Python3-nipy
-
Analysis of structural and functional neuroimaging data
-
Python3-nipype
-
Neuroimaging data analysis pipelines in Python3
-
Python3-nitime
-
timeseries analysis for neuroscience data (nitime)
-
Python3-pydicom
-
DICOM medical file reading and writing (Python 3)
-
Python3-pyxid
-
interface for Cedrus XID and StimTracker devices
-
Python3-surfer
-
visualize Freesurfer's data in Python3
-
Sigviewer
-
GUI viewer for biosignals such as EEG, EMG, and ECG
-
Sofa-apps
-
GUI for the Simulation Open Framework Architecture (SOFA)
-
Teem-apps
-
Tools to process and visualize scientific data and images - command line tools
-
Tifffile
-
Read and write image data from and to TIFF files
-
Voxbo
-
processing, statistical analysis, and display of brain imaging data
-
Vrrender
-
DICOM viewer
-
Vtk-dicom-tools
-
DICOM for VTK - tools
-
Xmedcon
-
Medical Image (DICOM, ECAT, ...) conversion tool (GUI)
Official Debian packages with lower relevance
-
Cmtk
-
Computational Morphometry Toolkit
-
Connectomeviewer
-
Interactive Analysis and Visualization for MR Connectomics
-
Elastix
-
toolbox for rigid and nonrigid registration of images
-
Illustrate
-
cartoonish representations of large biological molecules
-
Imagemagick
-
??? missing short description for package imagemagick :-(
-
Imview
-
Image viewing and analysis application
-
Orthanc-dicomweb
-
Plugin to extend Orthanc with support of WADO and DICOMweb
-
Orthanc-gdcm
-
DICOM transcoder/decoder for Orthanc using GDCM (notably for JPEG2k)
-
Orthanc-imagej
-
ImageJ plugin to import images from Orthanc
-
Orthanc-mysql
-
Plugins to use MySQL or MariaDB as a database back-end to Orthanc
-
Orthanc-neuro
-
Neuroimaging plugin for Orthanc
-
Orthanc-postgresql
-
Plugins to use PostgreSQL as a database back-end to Orthanc
-
Orthanc-webviewer
-
Web viewer of medical images for Orthanc
-
Paraview
-
Parallel Visualization Application
-
Pngquant
-
PNG (Portable Network Graphics) image optimising utility
-
Science-workflow
-
workflow management systems useful for scientific research
-
Trimage
-
GUI and command-line interface to optimize image files
Debian packages in contrib or non-free
-
Bart-cuda
-
tools for computational magnetic resonance imaging
-
Fsl
-
transitional dummy package
-
Vmtk
-
the Vascular Modeling Toolkit
Packaging has started and developers might try the packaging code in VCS
-
Bioimagesuite
-
integrated image analysis software suite
-
Bioimagexd
-
Analyzing, processing and visualizing of multi dimensional microscopy images
-
Cellprofiler
-
quantitatively measure phenotypes from images automatically
-
Crea
-
base library of the creaTools medical image processing suite
-
Dicoogle
-
Java Advanced Imaging API reference implementation
-
Fiji
-
"batteries-included" distribution of ImageJ
-
Freesurfer
-
analysis and visualization of functional brain imaging data
-
Incf-nidash-oneclick-clients
-
utility for pushing DICOM data to the INCF datasharing server
-
Insightapplications
-
InsightToolKit (ITK) based medical imaging applications
-
Jist
-
Java Image Science Toolkit
-
Kradview
-
medical image viewer for DICOM images
-
Libdcm4che-java
-
Clinical Image and Object Management
-
Mayam
-
Cross-platform DICOM Viewer
-
Micromanager
-
Microscopy Software
-
Mipav
-
quantitative analysis and visualization of medical images
-
Mni-colin27-nifti
-
Talairach stereotaxic space template
-
Openelectrophy
-
data analysis GUI for intra- and extra-cellular recordings
-
Openmeeg-tools
-
openmeeg library -- command line tools
-
Slicer
-
software package for visualization and image analysis - main application
-
Stabilitycalc
-
evaluate fMRI scanner stability
-
Via-bin
-
tools for volumetric image analysis
-
Visit
-
interactive parallel visualization and graphical analysis tool
-
Xnat
-
platform for data management and productivity tasks in neuroimaging
Unofficial packages built by somebody else
-
Cdmedicpacs
-
web interface to PACS to access DICOM study images
-
Mni-autoreg
-
MNI average brain (305 MRI) stereotaxic registration model
-
Mni-n3
-
MNI Non-parametric Non-uniformity Normalization
-
Opendicom.net
-
API to DICOM in C# for Mono
No known packages available but some record of interest (WNPP bug)
-
Devide
-
Delft Visualization and Image processing Development Environment
-
Dtitk
-
DTI spatial normalization and atlas construction toolkit
-
Eeglab
-
toolbox for processing and visualization of electrophysiological data
-
Isis
-
I/O framework for neuroimaging data
-
Jemris
-
high performance computing MRI simulator
-
Opensourcepacs
-
medical image referral, archiving, routing and viewing system
No known packages available
-
Blox
-
medical imaging and visualization program
-
Brainvisa
-
image processing factory for MR images
-
Dcm4chee
-
Clinical Image and Object Management (enterprise)
-
Dicom4j
-
Java framework for Dicom
-
Drjekyll
-
interactive voxel editor for viewing and editing three-dimensional images
-
Dti-query
-
dynamic queries of the white matter brain pathways
-
Ecg2png
-
convert scanned electrocardiograms into PNG format
-
Gimias
-
Graphical Interface for Medical Image Analysis and Simulation
-
Hid
-
database management system for clinical imaging
-
Maris
-
package suite for Radiological Workflow
-
Medisnap
-
photograph, manage, view, compare, document and archive medical photos
-
Mesa-test-tools
-
IHE Test Software for Radiology
-
Miview
-
Medical Images viewer and converter
-
Mni-icbm152-nlin-2009
-
MNI stereotaxic space human brain template
-
Mrisim
-
simulator for magnetic resonance imaging data
-
Omero
-
coming standard LIMS for microscopy images
-
Piano
-
medical image processing library for surgical planning
-
Pymeg
-
suite for analysis of magnetoencephalography (MEG) data
-
Stir
-
Software for Tomographic Image Reconstruction
-
Tempo
-
3D visualization of brain electrical activity
This metapackage will install Debian packages which might be useful
for developing applications for medical image processing and
visualization.
Official Debian packages with high relevance
-
Cimg-dev
-
powerful image processing library
-
Ctn-dev
-
Development files for Central Test Node, a DICOM implementation
-
Gmic
-
GREYC's Magic for Image Computing
-
Libbart-dev
-
Development files for BART
-
Libbiosig-dev
-
I/O library for biomedical data - development files
-
Libcamitk-dev
-
Computer Assisted Medical Intervention Tool Kit - development
-
Libcifti-dev
-
development files for CiftiLib
-
Libedf-dev
-
European Data Format library - devel
-
Libgdcm2-dev
-
Grassroots DICOM development libraries and headers
-
Libgdf-dev
-
IO library for the GDF -- development library
-
Libgiftiio-dev
-
IO library for the GIFTI cortical surface data format - headers
-
Libinsighttoolkit5-dev
-
Image processing toolkit for registration and segmentation - development
-
Libismrmrd-dev
-
development files for ISMRMRD
-
Libmaxflow-dev
-
Development files for the maxflow-mincut algorithm
-
Libmdc2-dev
-
??? missing short description for package libmdc2-dev :-(
-
Libmia-2.4-dev
-
library for 2D and 3D gray scale image processing, development files
-
Libmialm-dev
-
Development files for the MIA landmark library
-
Libminc-dev
-
MNI medical image format development environment
-
Libnifti2-dev
-
IO libraries for the NIfTI-1 data format (development)
-
Libodil-dev
-
C++11 library for the DICOM standard (development files)
-
Libopencv-dev
-
development files for opencv
-
Libopenigtlink-dev
-
Open IGT Link is a simple network protocol - development
-
Libopenslide-dev
-
Development files for the OpenSlide library
-
Libpapyrus3-dev
-
DICOM compatible file format library
-
Libsight-dev
-
Sight header files
-
Libteem-dev
-
Tools to process and visualize scientific data and images - development
-
Libvigraimpex-dev
-
development files for the C++ computer vision library
-
Libvistaio-dev
-
Development files for the libvistaio library
-
Libvolpack1-dev
-
fast volume rendering library (development package)
-
Libvtk-dicom-dev
-
DICOM for VTK - dev
-
Libvtk9-dev
-
VTK header files
-
Libxdf-dev
-
C++ library for loading XDF files (headers and static lib)
-
Octave-bart
-
Octave bindings for BART
-
Octave-dicom
-
manipulate DICOM files in Octave
-
Octave-gdf
-
IO library for the GDF -- Octave interface
-
Odin
-
develop, simulate and run magnetic resonance sequences
-
Python3-biosig
-
Python3 bindings for BioSig library
-
Python3-bioxtasraw
-
process biological small angle scattering data
-
Python3-brian
-
simulator for spiking neural networks
-
Python3-dcmstack
-
DICOM to NIfTI conversion - python3 package
-
Python3-dipy
-
Python library for the analysis of diffusion MRI datasets
-
Python3-gdcm
-
Grassroots DICOM Python bindings
-
Python3-imageio
-
library for reading and writing image data (Python 3)
-
Python3-mia
-
Python-3 bindings for the MIA image processing library
-
Python3-mne
-
Python modules for MEG and EEG data analysis
-
Python3-nibabel
-
Python3 bindings to various neuroimaging data formats
-
Python3-nipy
-
Analysis of structural and functional neuroimaging data
-
Python3-nipype
-
Neuroimaging data analysis pipelines in Python3
-
Python3-nitime
-
timeseries analysis for neuroscience data (nitime)
-
Python3-openslide
-
Python 3 wrapper for reading whole slide image files
-
Python3-pydicom
-
DICOM medical file reading and writing (Python 3)
-
Python3-pyxnat
-
Interface to access neuroimaging data on XNAT servers
-
Python3-torchvision
-
Datasets, Transforms and Models specific to Computer Vision
-
Python3-vigra
-
Python3 bindings for the C++ computer vision library
Official Debian packages with lower relevance
-
Libcamp-dev
-
C++ multi-purpose reflection library (development files)
-
Libeegdev-dev
-
Biosignal acquisition device library (Development files)
-
Libfreeimage-dev
-
Support library for graphics image formats (development files)
-
Libics-dev
-
Image Cytometry Standard file reading and writing (devel)
-
Liblimereg-dev
-
Library for lightweight image registration [development files]
-
Libnifti-doc
-
NIfTI library API documentation
-
Libxdffileio-dev
-
Library to read/write EEG data file formats (development files)
-
Tifffile
-
Read and write image data from and to TIFF files
Debian packages in contrib or non-free
-
Libvmtk-dev
-
shared links and header files for vmtk
-
Python-vmtk
-
Python interface for vmtk
Packaging has started and developers might try the packaging code in VCS
-
Emokit
-
Emotiv EPOC headset Python interface
-
Libbio-formats-java
-
reading and writing proprietary microscopy image data and metadata
-
Libctk-dev
-
toolkit for medical imaging application development - devel
-
Libopenmeeg-dev
-
openmeeg library -- development files
-
Libopenslide-java
-
java wrapper for reading whole slide image files
-
Libvia-dev
-
library for volumetric image analysis
Unofficial packages built by somebody else
-
Libmni-perllib-perl
-
The MNI Perl Library
This metapackage contains dependencies for software and that could
be useful ro run a medical laboratory.
Official Debian packages with high relevance
-
Opencfu
-
count cell colonies (CFUs) on agar plates by processing digital pictures
-
Orthanc-wsi
-
Whole-slide imaging support for Orthanc (digital pathology)
Packaging has started and developers might try the packaging code in VCS
-
Openfreezer
-
Laboratory analysis, research and investigation software application
No known packages available
-
Catissuesuite
-
tool for biospecimen inventory management
-
Openelis
-
Enterprise Laboratory Information System
This metapackage will install tools that are useful for radiation
oncology.
Official Debian packages with high relevance
-
Orthanc-wsi
-
Whole-slide imaging support for Orthanc (digital pathology)
-
Simrisc
-
simulation model for breast/lung cancer risk
Official Debian packages with lower relevance
-
Python3-dicompylercore
-
core radiation therapy modules for DICOM / DICOM RT used by dicompyler
Packaging has started and developers might try the packaging code in VCS
-
Uw-prism
-
software tools for radiation therapy planning
No known packages available
-
Planunc
-
tools for radiotherapy treatment planning
This metapackage contains dependencies for a
collection of software and documentation which is useful for
pharmaceutical research.
Official Debian packages with high relevance
-
Chemtool
-
chemical structures drawing program
-
R-cran-dosefinding
-
Planning and Analyzing Dose Finding experiments
-
R-cran-rpact
-
Confirmatory Adaptive Clinical Trial Design and Analysis
This metapackage contains dependencies for a
collection of software and documentation which is useful for
medical physicists in radiation oncology, diagnostics imaging
and related fields.
Official Debian packages with high relevance
-
Biosig-tools
-
format conversion tools for biomedical data formats
-
Gdf-tools
-
IO library for the GDF -- helper tools
-
Octave
-
GNU Octave language for numerical computations
-
Paw
-
Physics Analysis Workstation - a graphical analysis program
-
Paw++
-
Physics Analysis Workstation (Lesstif-enhanced version)
-
R-base
-
GNU R statistical computation and graphics system
Official Debian packages with lower relevance
-
Libbiosig-dev
-
I/O library for biomedical data - development files
-
Octave-biosig
-
Octave bindings for BioSig library
-
Paw-demos
-
Physics Analysis Workstation examples and tests
-
Python3-biosig
-
Python3 bindings for BioSig library
-
Python3-multipletau
-
multiple-tau algorithm for Python3/NumPy
No known packages available but some record of interest (WNPP bug)
-
Gate
-
Geant4 Application for Emission Tomography
-
Openvibe
-
platform for the design, test and use of BCI
This metapackage contains dependencies for a collection of software
which might be helpful for practitioners to manage their practice.
Official Debian packages with high relevance
-
Entangle
-
Tethered Camera Control & Capture
-
Freediams
-
pharmaceutical drug prescription and interaction manager
-
Freemedforms-emr
-
electronic medical record manager
-
Ginkgocadx
-
Medical Imaging Software and complete DICOM Viewer
-
Gnumed-client
-
medical practice management - Client
-
Gnumed-server
-
medical practice management - server
-
Libchipcard-tools
-
tools for accessing chipcards
-
Orthanc
-
Lightweight, RESTful DICOM server for medical imaging
-
Orthanc-wsi
-
Whole-slide imaging support for Orthanc (digital pathology)
-
Oscar
-
Open Source CPAP Analysis Reporter (OSCAR)
-
Qrisk2
-
cardiovascular disease risk calculator
-
R-cran-medadherence
-
GNU R Medication Adherence: Commonly Used Definitions
Official Debian packages with lower relevance
-
Libctapimkt1
-
Read German Krankenversichertenkarte and eGK
Packaging has started and developers might try the packaging code in VCS
-
Freeshim
-
opensource electronic medical device interface
-
Openemr
-
Comprehensive medical practice management
-
Thera-pi
-
organization and management of outpatient clinics and rehabilitation-medicine companies
Unofficial packages built by somebody else
-
Elementalclinic
-
Electronical Medical Health record system for mental health
-
Freemed
-
Electronic Medical Record and Practice Management system
-
Tinyheb
-
billing system for midwives
No known packages available but some record of interest (WNPP bug)
-
Elexis
-
medical practice managemant system for use in Switzerland
-
Openrep
-
software for homeopathic repertorization and viewing materia medicae
No known packages available
-
Clearhealth
-
Medical practice management system
-
Freeb
-
Medical Bill formating module
-
Medintux
-
Medical practice management system
-
Mirrormed
-
EHR and practice management system
-
Mirth
-
HL7 integration engine
-
Openpms
-
medical billing, scheduling, and account management system
-
Proteus
-
clinical decision support guidelines model
-
Remitt
-
preparing and submitting medical billing data
-
Resmedicinae
-
comprising software solution for use in medicine
-
Sqlclinic
-
intranet solution for Saint Vincents Catholic Medical Centers of New York
This metapackage contains dependencies for a collection of software
which might be helpful for psychological research.
Official Debian packages with high relevance
-
Orthanc-neuro
-
Neuroimaging plugin for Orthanc
-
Praat
-
program for speech analysis and synthesis
-
Psignifit
-
Fitting and testing hypotheses about psychometric functions
-
Psychopy
-
environment for creating psychology stimuli in Python
-
Python3-bioxtasraw
-
process biological small angle scattering data
-
R-cran-foreign
-
GNU R package to read/write data from other stat. systems
-
R-cran-psy
-
GNU R procedures for psychometrics
-
R-cran-psych
-
GNU R procedures for psychological, psychometric, and personality research
-
R-cran-psychometric
-
GNU R applied psychometric theory
-
R-cran-psychotree
-
GNU R recursive partitioning based on psychometric models
-
R-cran-psyphy
-
functions for analyzing psychophysical data in GNU R
Official Debian packages with lower relevance
-
Python-pyepl
-
module for coding psychology experiments in Python
-
Python3-bids-validator
-
validator for the Brain Imaging Data Structure (BIDS) datasets
-
Python3-bmtk
-
development package for building, simulating and analysing large-scale networks
-
Python3-pynwb
-
Python library for working with Neurodata in the NWB format
-
Science-psychophysics
-
Debian Science packages for Psychophysics
This metapackage will install tools that are useful for
rehabilitation and therapy.
Official Debian packages with high relevance
-
Sitplus
-
??? missing short description for package sitplus :-(
Official Debian packages with lower relevance
-
Aghermann
-
Sleep-research experiment manager
This metapackage will install tools that are useful for
medical research.
Official Debian packages with high relevance
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R-cran-rpact
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Confirmatory Adaptive Clinical Trial Design and Analysis
No known packages available but some record of interest (WNPP bug)
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Openclinica
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electronic data capture and clinical data management
This metapackage will install packages which are helpful to do statistics
with a special focus on tasks in medical care.
Official Debian packages with high relevance
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R-bioc-edger
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Empirical analysis of digital gene expression data in R
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R-bioc-limma
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linear models for microarray data
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R-bioc-multtest
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Bioconductor resampling-based multiple hypothesis testing
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R-bioc-qvalue
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GNU R package for Q-value estimation for FDR control
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R-cran-ade4
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GNU R analysis of ecological data
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R-cran-beeswarm
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bee swarm plot, an alternative to stripchart
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R-cran-pvclust
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Hierarchical Clustering with P-Values via Multiscale Bootstrap
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R-cran-randomforest
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GNU R package implementing the random forest classificator
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R-cran-rwave
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GNU R time-frequency analysis of 1-D signals
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R-cran-snowfall
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GNU R easier cluster computing (based on snow)
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R-cran-waveslim
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GNU R wavelet routines for 1-, 2- and 3-D signal processing
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R-cran-wavethresh
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GNU R wavelets statistics and transforms
Official Debian packages with lower relevance
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Science-statistics
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Debian Science Statistics packages
Packaging has started and developers might try the packaging code in VCS
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Rstudio
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GNU R IDE
This metapackage will install tools for several purposes in health care.
Currently it contains some simple programs for Personal Health.
Official Debian packages with high relevance
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Cronometer
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CRON-o-Meter - Exercise and nutrient intake tracker
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Cycle
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calendar program for women
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Edfbrowser
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viewer for biosignal storage files such as bdf and edf
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Galileo
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Utility to securely synchronize a Fitbit device with the Fitbit web service
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Hunspell-de-med
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German medical dictionary for hunspell
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Hunspell-en-med
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English medical dictionary for hunspell
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Nut-nutrition
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??? missing short description for package nut-nutrition :-(
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Nutsqlite
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Dietary nutrition analysis software
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Pcalendar
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track menstrual cycles and predict fertility periods
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Pondus
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personal weight manager for GTK+2
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Python3-fitbit
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FitBit REST API Client Implementation - Python 3
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Quitcount
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Small tool which may help yourself quit smoking
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R-cran-fitbitscraper
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Import your Fitbit data from the Fitbit's website into R
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R-cran-fitcoach
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R package for analysis and retrieve data of Fitbit
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Wgerman-medical
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German medical dictionary words for /usr/share/dict
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Workrave
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Repetitive Strain Injury prevention tool
Official Debian packages with lower relevance
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Entangle
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Tethered Camera Control & Capture
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Goldencheetah
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set of analysis tools for cycling performance
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Mencal
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menstruation calendar
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Oscar
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Open Source CPAP Analysis Reporter (OSCAR)
Debian packages in contrib or non-free
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Mssstest
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Normalisation of disease scores for patients with Multiple Sclerosis
Packaging has started and developers might try the packaging code in VCS
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Pesco
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Cognitive stimulation tool for elderly or cognitively impaired
This metapackage will install Debian packages that might be helpful
for typesetting and publishing in medical care and structural
biology.
Official Debian packages with high relevance
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King
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interactive system for three-dimensional vector graphics
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Texlive-latex-extra
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??? missing short description for package texlive-latex-extra :-(
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Texlive-science
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??? missing short description for package texlive-science :-(
Official Debian packages with lower relevance
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Biber
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Much-augmented BibTeX replacement for BibLaTeX users
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Bibus
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bibliographic database
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Jabref-plugin-oo
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??? missing short description for package jabref-plugin-oo :-(
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Kbibtex
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BibTeX editor for KDE
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R-cran-qqman
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R package for visualizing GWAS results using Q-Q and manhattan plots
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