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This repository has been archived by the owner on Aug 12, 2021. It is now read-only.
The MSigDB is a collection of annotated gene sets, it include 8 major collections:
* H: hallmark gene sets
* C1: positional gene sets
* C2: curated gene sets
* C3: motif gene sets
* C4: computational gene sets
* C5: GO gene sets
* C6: oncogenic signatures
* C7: immunologic signatures
Users can use `enricher` and `GSEA` function to analyze gene set collections downloaded from Molecular Signatures Database ([MSigDb](http://www.broadinstitute.org/gsea/msigdb/index.jsp)). [clusterProfiler](https://www.bioconductor.org/packages/clusterProfiler) provides a function, `read.gmt`, to parse the [gmt file](www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#GMT:_Gene_Matrix_Transposed_file_format_.28.2A.gmt.29) into a _TERM2GENE_ `data.frame` that is ready for both `enricher` and `GSEA` functions.