Software for Genomic Data Analysis

Many good software modules for statistical analysis of genomic data are offered as open source (free but copyright protected). The main platforms (e.g. application software) for these are R (free, open source) and MatLab (commercial). Both R and MatLab are available on UNIX/Linux, Windows (95/98/NT4/2000/ME on Intel-type machines), and MacOS (7.6 or later for MatLab, 8.6 or later for R). Below are some highlights. Follow links to find other modules and packages.

Many sites have software and data on the same page. Check our Genomic Data page.

Quantitative Trait Loci Software
Expression Networks
Gene Expression Microarray Software
The R Project (documentation, system download)
Yandell's R Introduction for Biologists
BioConductor site for bioinformatics software
BioPERL (PERL for Bioinformatics Applications)
Evolution Highway
Animal Breeding & Genetics Hub
BioConductor site for bioinformatics software
Bioinformatics World
Genetic Linkage Analysis Software
Statistical Genomics Data
Reference List with Links

Gene Expression Microarray Software

HDBStat! (UAB Statistical Genetics)
ChipST2C: significance testing to cluster analysis ("ST2C") of DNA microarray data analysis (Lief Peterson Software Lab at Baylor College of Medicine)
The Analysis Of Gene Expression Data: Methods and Software, ed. by Giovanni Parmigiani et al. (2003)
Gary Churchill's Statistical Genetics Group, Jackson Labs
UPCI GEDA Web Tool and GEDS Simulator
GeneSifter Data Center
GeneX Analysis Tools, NCGR and UC Irvine
Tony Long's Statistical Analysis and Molecular Biology Tools, UC Irvine
Leif Peterson's Genetic Epidemiology (GenEpi), Baylor College of Medicine
Terry Speed's Software Page, UC Berkeley
Rob Tibshirani's Significance Analysis of Microarrays (SAM), Stanford U
Wing Wong's dChip (Li Wong 2000 PNAS), Harvard U
PowerAtlas (UAB)
QUANTO(USC)
Gene Expression Data Analysis (GEDA), UW-Madison Biostatistics & Medical Informatics Department
- GEDA's R System Software for Microarray Data Analysis
- GEDA Related Sites (includes software links)
Stanford Microarray Database (SMD)
NIH/NHGRI Microarray Project

R System Software for Microarrray Data Analysis

Microarray analysis software has been developed under the R System, which is freely available for Linux, Windows and Mac OSX. See other software, data and related links at GEDA.

Adaptive Gene Picking for Microarray Expression Data Analysis (pickgene package for analysis used in Lin et al. (2003)): now available directly from BioConductor
sma (Terry Speed's group)

Return to Statistical Genomics Page

Brian Yandell (www.stat.wisc.edu/~yandell)