[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)
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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:
http://bioconductor.org/packages/2.13/bioc/html/gage.html
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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