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aertslab / SCENIC

SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
http://scenic.aertslab.org
GNU General Public License v3.0
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importModulesGmt doubt #215

Closed rosanababu closed 2 years ago

rosanababu commented 3 years ago

Hi aertslab,

Could you please help me to clarify a small doubt?

Can I use output from pyscenic grn step (adjacencies.tsv) as input for below steps to convert regulons stored as incidence matrix to gene sets (e.g. list of genes)?

regulons <- importModulesGmt(file.path(pyScenicDir, "adjacencies.tsv")) regulons <- geneIds(regulons) or GRNBoost_linkList <- importArboreto(file.path(pyScenicDir, "adjacencies.tsv")) regulons_genelist <- regulonsToGeneLists(GRNBoost_linkList)

Looking forward for your kind reply