The Molecular Signatures Database (MSigDB) in a tidy data frame.
This is the updated version of the archived repo of @stephenturner
Current version: v6.2 (July 2018).
# 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)
See the package vignette for more.
library(dplyr)
library(msigdf)
vignette("msigdf")
msigdf.human %>%
filter(category_code=="hallmark") %>%
head
# A tibble: 6 x 4
category_code category_subcode geneset symbol
<chr> <chr> <chr> <chr>
1 hallmark all HALLMARK_TNFA_SIGNALING_VIA_NFKB JUNB
2 hallmark all HALLMARK_TNFA_SIGNALING_VIA_NFKB CXCL2
3 hallmark all HALLMARK_TNFA_SIGNALING_VIA_NFKB ATF3
4 hallmark all HALLMARK_TNFA_SIGNALING_VIA_NFKB NFKBIA
5 hallmark all HALLMARK_TNFA_SIGNALING_VIA_NFKB TNFAIP3
6 hallmark all HALLMARK_TNFA_SIGNALING_VIA_NFKB PTGS2
msigdf.human %>% filter(geneset=="KEGG_NON_HOMOLOGOUS_END_JOINING")
# A tibble: 14 x 4
category_code category_subcode geneset symbol
<chr> <chr> <chr> <chr>
1 c2 cp KEGG_NON_HOMOLOGOUS_END_JOINING XRCC4
2 c2 cp KEGG_NON_HOMOLOGOUS_END_JOINING MRE11A
3 c2 cp KEGG_NON_HOMOLOGOUS_END_JOINING POLL
4 c2 cp KEGG_NON_HOMOLOGOUS_END_JOINING POLM
5 c2 cp KEGG_NON_HOMOLOGOUS_END_JOINING LOC731751
6 c2 cp KEGG_NON_HOMOLOGOUS_END_JOINING NHEJ1
7 c2 cp KEGG_NON_HOMOLOGOUS_END_JOINING LIG4
8 c2 cp KEGG_NON_HOMOLOGOUS_END_JOINING FEN1
9 c2 cp KEGG_NON_HOMOLOGOUS_END_JOINING DNTT
10 c2 cp KEGG_NON_HOMOLOGOUS_END_JOINING XRCC5
11 c2 cp KEGG_NON_HOMOLOGOUS_END_JOINING RAD50
12 c2 cp KEGG_NON_HOMOLOGOUS_END_JOINING XRCC6
13 c2 cp KEGG_NON_HOMOLOGOUS_END_JOINING PRKDC
See the package vignette for more.