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Bioinformatics Tools

Free Microarray Analysis Tools

BioConductor
By BioConductor Team
It is Primarily based on the R programming language. It aims to provide access to a wide range of powerful statistical and graphical methods for the analysis of genomic data. Analysis packages are available for: pre-processing Affymetrix and cDNA array data.

Cleaver 1.0
By Stanford Biomedical Informatics
Classification (discriminant analysis), K-means clustering, PCA

Cluster Identification Tool (CIT)
By Van Andel Research Institute
Statistical discrimination metric and permutation analysis to identify clusters of genes or individual genes that best differentiate experimental groups.

Gene Cluster 2.0
By Whitehead Institute Centre for genome research filter and preprocess data in a variety of ways; Self-Organizing Map; unsupervised classification by weighted voting (WV) and k-nearest neighbors (KNN) algorithms, gene selection and permutation test methods

PAM (Prediction Analysis for Microarrays)
By Tibshirani Lab; Department of Statistics, Stanford University
Performs sample classification from gene expression data, Estimates prediction error via cross-validation, Provides a list of significant genes whose expression characterizes each diagnostic class

SAM (Significance Analysis of Microarrays)
By Tibshirani Lab; Department of Statistics, Stanford University
Correlates gene expression data to a wide variety of clinical parameters including  treatment, diagnosis categories, survival time and time trends; Provides estimate of False Discovery Rate for multiple testing.

OBRC: Online Bioinformatics Resources Collection

Text-mining tools

Semantic Gene Organizer

Gene-set Cohesion Analysis Tool

GeneIndexer

Chilibot

ArrowSmith

GoPubMed

iHOP

String

Gene Expression tools

GeneSpring

GeneMaths

WebGestalt

Online courses and tutorials

  • Statistics for Genomics by Rafael Irizarry: website 
  • Python for Biologists tutorial: Tutorial
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Last Updated: 7/22/13