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Bioinformatics Tools and Resources

Gene Expression 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.

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.

GeneSpring

GeneMaths

WebGestalt

Text-mining Tools

Semantic Gene Organizer

Geneset Cohesion Analysis Tool

GeneIndexer

Chilibot

ArrowSmith

GoPubmed

iHOP

STRING

Visualization Tools

Cytoscape

Databases

GeneNetwork

GEMMA

BioGPS

Allen Brain Atlas

Online Courses and Tutorials

  • Statistics for Genomics by Rafael Irizarry: Website 
  • Python for Biologists: Tutorial
  • Problem solving for Bioinformatics by Rosalind: Website
  • Python course by Code Academy: Website
  • PLoS Open Access Book on Translational Bioinformatics: Website
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Last Updated: 7/17/14