MSigDF

The Molecular Signatures Database (MSigDB) in a tidy data frame.

This is the updated version of the archived repo of @stephenturner

Current version: v2026.1.

Important Notices - MSigDB v2026.1 (Jan 2026) is based on gene annotation data from Ensembl Release 115 (September 2026). - Human realese notes: https://docs.gsea-msigdb.org/#MSigDB/Release_Notes/MSigDB_2026.1.Hs/ - Mouse release notes: https://docs.gsea-msigdb.org/#MSigDB/Release_Notes/MSigDB_2026.1.Mm/

Installation

# Install devtools if you don't already have it
install.packages("devtools")

# Just get the data
devtools::install_github("toledoem/msigdf")

# Get the data and build the vignette (requires tidyverse, knitr, rmarkdown)
devtools::install_github("toledoem/msigdf", build_vignettes = TRUE)

Example usage

See the package vignette for more examples.

library(dplyr)
library(msigdf)
#vignette("msigdf")

msigdf.human %>%
  filter(category_code=="h") %>%
  head

# A tibble: 6 x 4
  category_code category_subcode geneset                          symbol
  <chr>         <chr>            <chr>                            <chr>
1 h      all              HALLMARK_TNFA_SIGNALING_VIA_NFKB JUNB
2 h      all              HALLMARK_TNFA_SIGNALING_VIA_NFKB CXCL2
3 h      all              HALLMARK_TNFA_SIGNALING_VIA_NFKB ATF3
4 h      all              HALLMARK_TNFA_SIGNALING_VIA_NFKB NFKBIA
5 h      all              HALLMARK_TNFA_SIGNALING_VIA_NFKB TNFAIP3
6 h      all              HALLMARK_TNFA_SIGNALING_VIA_NFKB PTGS2 

> msigdf.human %>% 
    filter(geneset=="KEGG_NON_HOMOLOGOUS_END_JOINING") %>% 
      group_by(category_subcode) %>% 
        top_n(n = 10)

Since now there are legacy and KEGG gene sets

Selecting by symbol
# A tibble: 20 × 4
# Groups:   category_subcode [2]
   category_code category_subcode geneset                         symbol
   <chr>         <chr>            <chr>                           <chr>
 1 c2            cp.kegg_legacy   KEGG_NON_HOMOLOGOUS_END_JOINING LIG4
 2 c2            cp.kegg_legacy   KEGG_NON_HOMOLOGOUS_END_JOINING MRE11
 3 c2            cp.kegg_legacy   KEGG_NON_HOMOLOGOUS_END_JOINING NHEJ1
 4 c2            cp.kegg_legacy   KEGG_NON_HOMOLOGOUS_END_JOINING POLL
 5 c2            cp.kegg_legacy   KEGG_NON_HOMOLOGOUS_END_JOINING POLM
 6 c2            cp.kegg_legacy   KEGG_NON_HOMOLOGOUS_END_JOINING PRKDC
 7 c2            cp.kegg_legacy   KEGG_NON_HOMOLOGOUS_END_JOINING RAD50
 8 c2            cp.kegg_legacy   KEGG_NON_HOMOLOGOUS_END_JOINING XRCC4
 9 c2            cp.kegg_legacy   KEGG_NON_HOMOLOGOUS_END_JOINING XRCC5
10 c2            cp.kegg_legacy   KEGG_NON_HOMOLOGOUS_END_JOINING XRCC6
11 c2            cp               KEGG_NON_HOMOLOGOUS_END_JOINING LIG4
12 c2            cp               KEGG_NON_HOMOLOGOUS_END_JOINING MRE11
13 c2            cp               KEGG_NON_HOMOLOGOUS_END_JOINING NHEJ1
14 c2            cp               KEGG_NON_HOMOLOGOUS_END_JOINING POLL
15 c2            cp               KEGG_NON_HOMOLOGOUS_END_JOINING POLM
16 c2            cp               KEGG_NON_HOMOLOGOUS_END_JOINING PRKDC
17 c2            cp               KEGG_NON_HOMOLOGOUS_END_JOINING RAD50
18 c2            cp               KEGG_NON_HOMOLOGOUS_END_JOINING XRCC4
19 c2            cp               KEGG_NON_HOMOLOGOUS_END_JOINING XRCC5
20 c2            cp               KEGG_NON_HOMOLOGOUS_END_JOINING XRCC6 

Building

Code for building this data is in folder data-raw

See the package vignette for more.

License

MSigDF by US is marked CC0 1.0