Debian Med Statistics packages

전체 전사체 시퀀싱 (RNA-seq)의 차등적 발현 분석과 생물학적 복제를 통한 디지털 유전자 발현 프로파일을 위한 생체전도체 패키지. 경험적 베이스 추정과 음이항 분포를 기반으로 한 정확한 검정을 사용합니다. 또한 다른 유형의 게놈 규모 카운트 데이터를 사용한 차등 신호 분석에도 유용합니다.

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.

이 패키지는 여러 가설을 동시에 테스트하여 얻은 p 값 리스트를 가져와 해당 q 값을 추정합니다. 테스트의 q 값은 해당 특정 테스트가 중요하다고 판단될 때 방생하는 잘못된 긍정 비율 (잘못된 발견률이라고 부른다)을 측정합니다. 다양한 플롯이 자동으로 생성되므로 합리적인 유익성 구분이 가능합니다. 최근 이 소프트웨어에서 추정된 q 값의 보수적인 정확도에 대한 여러 수학적 결과가 표시되었습니다. 이 소프트웨어는 유전체하, 뇌 영상, 천체 물리학, 데이터 마이닝 분야에서 문제로 적용될 수 있습니다.

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 implements Breiman’s random forest algorithm (based on Breiman and Cutler’s original Fortran code) for classification and regression. It can also be used in unsupervised mode for assessing proximities among data points.

The technique uses multiple decision trees and combines their individual votes.

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.

이 메타패키지는 Debian Pure Blend "Debian Science"의 일부이며 통계와 관련된 패키지를 설치합니다. 이 태스크는 모든 과학 작업에 유용한 일반적인 태스크입니다. 통계 작성은 많은 R 패키지 뿐만 아니라 통계 작성에 유용한 다른 도구에서 결정됩니다. 게다가 과학 수학 작업은 모든 수학 관련 소프트웨어를 추가적으로 설치할 것을 제안합니다.

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.