msigdf's Introduction

MSigDF

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).

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.

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.

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