[BioC] GAGE/Pathview RNA-Seq Data Pathway and Gene-set Analysis Workflows

Luo Weijun luo_weijun at yahoo.com
Tue Oct 1 18:53:27 CEST 2013

There was a typo in the code lines, which has been fixed in the vignette of gage 2.11.5.
Typo: hnrnp.cnts==assay(gnCnt)
Correct: hnrnp.cnts=assay(gnCnt)


 Subject: GAGE/Pathview RNA-Seq Data Pathway and Gene-set Analysis Workflows
 To: bioconductor at r-project.org
 Date: Monday, September 30, 2013, 8:00 PM
 We just added a new vignette to the
 gage package (2.11.4), "RNA-Seq Data Pathway and Gene-set
 Analysis Workflows", demonstrates applications of
 GAGE/Pathview worklows in RNA-Seq data analysis. Please
 check it out at:
 We first cover a full workflow from preparation, reads
 counting, data preprocessing, gene set test, to pathway
 visualization in about 40 lines of codes. The same workflow
 can be used for GO analysis too. We also describe joint
 workflows, i.e. to do gene-level analysis using one of the
 major RNA-Seq analysis tools, DEseq/DEseq2, edgeR, limma and
 Cufflinks, and feed the results into GAGE/Pahview for
 pathway analysis or visualization. All these workflows are
 implemented in R/Bioconductor.
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