gmt2list

a gmt file. Examples are from MSigDB Collections.
A list of gene set could be find in the vignette of cogena

annofile


read Gene Matrix Transposed (gmt) file and output a list with the the first 
column as the names of items in the list. see 
<a href="http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats">Gene Matrix Transposed file format</a>
for more details.


cogena is a workflow for co-expressed gene-set enrichment analysis.
It aims to discovery smaller scale, but highly correlated cellular events that
may be of great biological relevance. A novel pipeline for drug discovery and
drug repositioning based on the cogena workflow is proposed. Particularly,
candidate drugs can be predicted based on the gene expression of disease-related
data, or other similar drugs can be identified based on the gene expression
of drug-related data. Moreover, the drug mode of action can be disclosed by
the associated pathway analysis. In summary, cogena is a flexible workflow for
various gene set enrichment analysis for co-expressed genes, with a focus on
pathway/GO analysis and drug repositioning.

Zhilong Jia

cogena

co-expressed gene-set enrichment analysis

gmt2list function


read Gene Matrix Transposed (gmt) file and output a list with the the first 
column as the names of items in the list. see 
<a href = 'http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats'>Gene Matrix Transposed file format</a>
for more details.


gmt2list: read gmt file as a list

Description

Usage

Arguments

Value

See Also

Examples