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. Comments and questions are welcome. Thanks!

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: 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. [[elided Yahoo spam]]