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Academic and Open Source Solutions
* software marked by an asterisk are used by PMGC

 Computational Genomics at Johns Hopkins
*Bowtie: an ultrafast, memory-efficient short read aligner
*TopHat: A spliced alignment system for RNA-seq experiments
*Cufflinks: A transcript assembler and abundance estimator for RNA-seq data


 *Burrows-Wheeler Aligner (BWA)
 Software package for mapping low-divergent sequences against a large reference genome.


 *SAMtools
 Provides utilities for manipulating alignments in the Sequence Alignment/Map (SAM) format.


 *bedtools
 A flexible suite of utilities for comparing genomic features.


 *Galaxy
 An open, web-based platform for data intensive biomedical research.


 BioPerl


 NCBI Data Mining Tools


 Broad Institute Center for Genome Research
*Integrative Genomics Viewer (IGV): visualization tool for genomic data
*Genome Analysis Toolkit (GATK): analysis of deep sequencing data
 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
 ArrayNorm: Java tool for normalization 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


 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
 SIFT: predict if an amino acid substitution affects function based on the degree of conservation
 Tm4 (Spotfinder, MIDAS, MADAM, MeV): manage and analyze microarray experiment data


 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 for custom microarray, based on GO nomenclature
 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