Question: multi-omics data gene set enrichment analysis
0
gravatar for email2mrna
21 months ago by
email2mrna0
email2mrna0 wrote:

I have multi-omics data (RNASeq, methylation and mutation) belonging to same sample and I want to do gene set enrichment analysis using all the data at once. What are the tool in R/Bioconductor to do gene set enrichment analysis of multiple omics dataset?

ADD COMMENTlink modified 21 months ago by EagleEye6.2k • written 21 months ago by email2mrna0
1
gravatar for Samuel Brady
21 months ago by
Samuel Brady280
Samuel Brady280 wrote:

GSOA incorporates multiple types of omic data at a time. See the paper and documentation to use it in R.

ADD COMMENTlink modified 21 months ago • written 21 months ago by Samuel Brady280
0
gravatar for EagleEye
21 months ago by
EagleEye6.2k
Sweden
EagleEye6.2k wrote:

Sorry non-R solution:

With GeneSCF you can keep all the list of genes (multiple files) in a single folder and provide that path in 'geneSCF_batch'. It will perform enrichment analysis for individual list and automatically creats output for every list.

Also choose the tool that regularly update the database/functional information. In that case GenrSCF will give you option of updating the database to current version using 'prepare_database' module before running enrichment analysis.

ADD COMMENTlink modified 21 months ago • written 21 months ago by EagleEye6.2k
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