oganm / msigdb

Molecular Signatures Database as a list

MSigDB

Houses gene lists from Broad Institute Molecular Signatures Database. They do want to keep track of their user counts so you might want to log in there as well. Note that there is an msigdbr package that is also uploaded to CRAN that provides similar funcitonality.

Installation

devtools::install_github('oganm/MSigDB')

Usage

library(MSigDB)
names(MSigDB)

## [1] "human" "mouse"

names(MSigDB$human)

##  [1] "C1"       "C2"       "C3"       "C4"       "C6"       "C7"      
##  [7] "C8"       "ARCHIVED" "C5"       "H"

head(names(MSigDB$human$H))

## [1] "HALLMARK_TNFA_SIGNALING_VIA_NFKB"    "HALLMARK_HYPOXIA"                   
## [3] "HALLMARK_CHOLESTEROL_HOMEOSTASIS"    "HALLMARK_MITOTIC_SPINDLE"           
## [5] "HALLMARK_WNT_BETA_CATENIN_SIGNALING" "HALLMARK_TGF_BETA_SIGNALING"

MSigDB$human$H$HALLMARK_PEROXISOME

##   [1] "ABCD3"    "ACOT8"    "ACOX1"    "ACSL1"    "ECH1"     "ECI2"    
##   [7] "EHHADH"   "GSTK1"    "HSD17B4"  "MLYCD"    "PEX11A"   "RETSAT"  
##  [13] "SLC27A2"  "PEX13"    "PEX14"    "SCP2"     "HSD3B7"   "GNPAT"   
##  [19] "ABCD2"    "SLC25A17" "PEX2"     "ACAA1"    "HAO2"     "HSD17B11"
##  [25] "CRAT"     "PEX11B"   "LONP2"    "IDH1"     "FIS1"     "PEX6"    
##  [31] "ABCB4"    "SOD1"     "ABCB1"    "ISOC1"    "YWHAH"    "EPHX2"   
##  [37] "ABCD1"    "HMGCL"    "ACSL5"    "ALDH9A1"  "DHCR24"   "ELOVL5"  
##  [43] "NUDT19"   "PRDX5"    "CTPS1"    "IDE"      "SLC23A2"  "PEX5"    
##  [49] "BCL10"    "NR1I2"    "TSPO"     "CNBP"     "MSH2"     "DHRS3"   
##  [55] "DIO1"     "SLC25A4"  "PRDX1"    "IDI1"     "HRAS"     "MVP"     
##  [61] "ABCC8"    "CLN6"     "CAT"      "ACSL4"    "IDH2"     "ABCC5"   
##  [67] "SOD2"     "SLC35B2"  "FDPS"     "ALB"      "FADS1"    "STS"     
##  [73] "SMARCC1"  "ITGB1BP1" "SIAH1"    "SLC25A19" "CDK7"     "RXRG"    
##  [79] "ALDH1A1"  "UGT2B17"  "CADM1"    "SERPINA6" "CLN8"     "RDH11"   
##  [85] "CTBP1"    "HSD11B2"  "TTR"      "ERCC3"    "ATXN1"    "SULT2B1" 
##  [91] "CRABP2"   "CRABP1"   "TOP2A"    "SCGB1A1"  "ERCC1"    "DLG4"    
##  [97] "PABPC1"   "FABP6"    "ABCB9"    "CACNA1B"  "SEMA3C"   "VPS4B"   
## [103] "CEL"      "ESR2"    
## attr(,"description")
##                                    GENESET 
## "Genes encoding components of peroxisome."

getMSigInfo function simply navigates to the broad institute website with the relevant data

getMSigInfo('HALLMARK_PEROXISOME','human')

msigdb's Issues

Fix the auto download selenium error