Skip to main content
. Author manuscript; available in PMC: 2015 Apr 28.
Published in final edited form as: Cell Physiol Biochem. 2014 Apr 28;33(5):1239–1260. doi: 10.1159/000358693

Table 1.

Resources for processing and analyzing genomics data

Software tools Microarray Analysis
1. (DAVID) v.6.7 http://david.abcc.ncifcrf.gov/
2. GenePattern 2.0 http://www.broadinstitute.org/cancer/software/genepattern/
3. Galaxy Project http://galaxyproject.org/
4. GenomeSpace http://www.genomespace.org
5. Bioconductor http://www.bioconductor.org/
6. Cytoscape http://www.cytoscape.org/
7. Ingenuity Pathways Analysis www.Ingenuity.com
8. GeneGO, MetaCore http://portal.genego.com/
9. Partek 6.3 www.partek.com
Software tools RNA-seq Analysis
1. Galaxy Project http://galaxyproject.org/
2. GenePattern 2.0 http://www.broadinstitute.org/cancer/software/genepattern/
3. R-workbench http://www.ebi.ac.uk/Tools/rcloud/
4. Palmapper http://raetschlab.org/suppl/palmapper
5. mTim http://raetschlab.org/suppl/mtim
6. rQuant http://raetschlab.org/suppl/rquant
7. rDiff http://cbio.mskcc.org/public/raetschlab/user/drewe/rdiff/