Skip to content

oganm/MSigDB

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

29 Commits
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Repository files navigation

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')

Releases

No releases published

Packages

No packages published