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bioinformatics
academic & open source
academic and open source solutions
* software marked by an asterisk are used by UHNMAC
The Centre for Computational Biology
Broad Institute Center for Genome Research
CellProfiler: high-throughput image analysis
GeneCruiser: expression analysis
GenePattern: expression analysis
Gene Set Enrichment Analysis (GSEA): expression analysis
Cytoscape Consortium
Cytoscape: visualizing networks and integrating interactions with profiles and data
CSIRO Mathematical and Information Sciences, Image Analysis Group
Spot: analsyis of microarray images
Graz University of Technology, Institute of Genomics and Bioinformatics
ArrayNorm: Java tool for normalisation and statistical analysis for microarray-experiment data
CARMAweb: web application for analysis of microarray data
Cluster Control: web-interface for distributing and monitoring applications on Linux cluster systems
Genesis: visualize and analyze a set of gene expression experiments
Pathway Explorer: drawing tool
Fred Hutchinson Cancer Research Center
Bioconductor: analysis and comprehension of genomic data
The Jackson Laboratory (Churchill's Group)
R/MAANOVA: microarray analysis
Rob Tibshirani's Group at Stanford
* SAM (Significance analysis for microarrays): genomic expression data mining
* PAM (Prediction analysis for micorarrays): class prediction and survival analysis for genomic expression
J.Craig Ventor Institute
Tm4 (Spotfinder, MIDAS, MADAM, MeV): manage and analyze microarray experiment data
Terry Speed's Berkeley Research Group
Statistics for Microarray Analysis (SMA): R package for analysis of cDNA microarray data
RMAExpress: generating RMA expression measures for Affymetrix data
University of California San Francisco
NOMAD: storing and querying microarray experiment results
Wayne State University Intelligent Systems & Bioinformatics Laboratory
* Onto-Express: translate lists of differentially regulated genes into functional profiles
* Onto-Compare: database providing functional analysis of arrays, based on GO nomenclature
Onto-Design: select genes based on their biological process, molecular function or cellular component
Onto-Translate: conversions of individual genes
Onto-Miner: annotations of known genes
* Pathway-Express: builds a list of all associated pathways of a gene of interest
Promoter-Express
Target Analysis Quantification (TAQ): accurately estimate initial template quantity
nsSNPCounter
Zhou Laboratory - University of Southern California
iArray: data mining and visualization platform for analysis of cross-platform microarray datasets