GenePattern – is a powerful genomic analysis platform that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks.
GenePattern offers a suite of tools to support a wide variety of RNA-seq analyses, including short-read mapping, identification of splice junctions, transcript and isoform detection, quantitation, and differential expression. The modules have been adapted from widely-used tools. GenePattern also provides pipelines that allow you to perform a number of multi-step RNA-seq analyses automatically.
- Differential Expression:Cufflinks.cuffdiff
- Genome Annotation:Cufflinks, Cufflinks.cuffcompare, Scripture
- Isoform Detection:Tophat
- RNA Quantitation:Cufflinks, Scripture
- Utilities:Bowtie.indexer, BamToSam, ExprToGct, SamToBam, SortSam
GenePattern is open access and is available here.