Debian Med Statistics packages

Bioconductor-Paket zur Differentialexpressionsanalyse eines vollkommen sequenzierten Transkriptom (RNA-seq) und digitalen Genexpressionsprofilen mit biologischer Replikation. Es verwendet empirische Bayes-Methoden und exakte Tests, die auf der negativen Binomialverteilung basieren. Es ist auch für die Differentialsignalanalyse mit anderen Typen von Zähldaten in der Größenordnung von Genomen verwendbar.

Microarrays are microscopic plates with carefully arranged short DNA strands and/or chemically prepared surfaces to which other DNA preferably binds. The amount of DNA binding at different locations of these chips, typically determined by a fluorescent dye, is to be interpreted. The technology is typically used with DNA that is derived from RNA, i.e to determine the activity of a gene and/or its splice variants. But the technology is also used to determine sequence variations in genomic DNA.

This Bioconductor package supports the analysis of gene expression microarray data, especially the use of linear models for analysing designed experiments and the assessment of differential expression. The package includes pre-processing capabilities for two-colour spotted arrays. The differential expression methods apply to all array platforms and treat Affymetrix, single channel and two channel experiments in a unified way.

Non-parametric bootstrap and permutation resampling-based multiple testing procedures (including empirical Bayes methods) for controlling the family-wise error rate (FWER), generalized family-wise error rate (gFWER), tail probability of the proportion of false positives (TPPFP), and false discovery rate (FDR). Several choices of bootstrap-based null distribution are implemented (centered, centered and scaled, quantile-transformed). Single-step and step-wise methods are available. Tests based on a variety of t- and F-statistics (including t-statistics based on regression parameters from linear and survival models as well as those based on correlation parameters) are included. When probing hypotheses with t-statistics, users may also select a potentially faster null distribution which is multivariate normal with mean zero and variance covariance matrix derived from the vector influence function. Results are reported in terms of adjusted p-values, confidence regions and test statistic cutoffs. The procedures are directly applicable to identifying differentially expressed genes in DNA microarray experiments.

Dieses Paket liefert eine Liste von p-Werten resultierend aus simultanen Tests von vielen Hypothesen und schätzt deren q-Werte. Der q-Wert eines Tests misst die Kosten der Proportionen von Falsch-zu-Richtig (genannt die »false discovery rate«, Fehlerentdeckungsrate), wenn der einzelne Test signifikant ist. Es werden automatisch unterschiedliche Aufzeichnungen generiert, die es einem Einzelnen erlauben ausschlaggebende »Cut-Off«-Werte zu liefern. Mehrere mathematische Ergebnisse haben in der Vergangenheit die konservative Genauigkeit der geschätzten q-Werte dieser Software gezeigt. Das Programm kann zur Problemlösung bei Genomik, Bildgebung des Gehirns, Astrophysik und Data Mining angewendet werden.

This GNU R package allows analysis of ecological data and contains exploratory and euclidean methods in environmental sciences.

It supports multivariate data analysis and graphical display.

Beeswarm is an add-on package for the R statistical environment. The bee swarm plot is a one-dimensional scatter plot like "stripchart", but with closely-packed, non-overlapping points.

pvclust is a package for assessing the uncertainty in hierarchical cluster analysis. It provides AU (approximately unbiased) p-values as well as BP (boostrap probability) values computed via multiscale bootstrap resampling.

RandomForest implementiert Breimans Random-Forest-Algorithmus (basierend auf dem ursprünglichen Fortran-Code von Breiman und Cutler) zur Klassifikation und Regression. Es kann auch im nicht überwachten Modus verwendet werden, um die Nähe von Datenpunkten zu bemessen.

Diese Technik verwendet multiple Entscheidungsbäume und kombiniert deren individuelle Stimmen.

A set of R functions which provide an environment for the Time-Frequency analysis of 1-D signals (and especially for the wavelet and Gabor transforms of noisy signals). It was originally written for Splus by Rene Carmona, Bruno Torresani, and Wen L. Hwang, first at the University of California at Irvine and then at Princeton University. Credit should also be given to Andrea Wang whose functions on the dyadic wavelet transform are included. Rwave is based on the book: "Practical Time-Frequency Analysis: Gabor and Wavelet Transforms with an Implementation in S", by Rene Carmona, Wen L. Hwang and Bruno Torresani (1998, eBook ISBN:978008053942), Academic Press.

Usability wrapper around snow for easier development of parallel R programs. This package offers e.g. extended error checks, and additional functions. All functions work in sequential mode, too, if no cluster is present or wished. Package is also designed as connector to the cluster management tool sfCluster, but can also used without it.

Basic wavelet routines for time series (1D), image (2D) and array (3D) analysis. The code provided here is based on wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet pairs (Selesnick 2001, 2002). All figures in chapters 4-7 of GSW (2001) are reproducible using this package and R code available at the book website(s) below.

Performs 1, 2 and 3D real and complex-valued wavelet transforms, nondecimated transforms, wavelet packet transforms, nondecimated wavelet packet transforms, multiple wavelet transforms, complex-valued wavelet transforms, wavelet shrinkage for various kinds of data, locally stationary wavelet time series, nonstationary multiscale transfer function modeling, density estimation.

Dieses Metapaket ist Teil des Debian Pure Blend »Debian Science« und installiert Pakete im Zusammenhang zum Begriff Statistiken. Dieser Task ist ein allgemeiner Task, welcher nützlich ist für alle wissenschaftlichen Arbeiten. Das Paket hängt von einer Reihe von R-Paketen ab, genau so wie von anderen Werkzeugen, die nützlich für die Anwendung von Statistik sind. Des weiteren ist der Task Mathematik-Wissenschaften empfohlen, um optionale Mathematik-Software zu installieren.

RStudio is an integrated development environment (IDE) for R. It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management.