Moonerss / genesets

a simple R data package for collected cancer associated gene lists

genesets: a simple R data package for collected cancer associated gene lists

The goal of genesets is to collect many useful gene sets for cancer bioinformatics analysis.

Installation

You can install the developing version of genesets from Github with:

devtools::install_github("Moonerss/genesets")

Getting started

All the gene sets list can be seen by:

library(genesets)
available_genesets()

[1] "CancerSEA" "Hallmark"  "Immport"

To search a special gene sets, you can use search_genesets():

search_genesets(keywords = "SEA")

[1] "CancerSEA"

The structure of each gene set like this:

str(CancerSEA)

List of 14
 $ angiogenesis   :'data.frame':    73 obs. of  2 variables:
  ..$ ensembl_gene_id: chr [1:73] "ENSG00000139567" "ENSG00000101384" "ENSG00000154188" "ENSG00000091879" ...
  ..$ symbol         : chr [1:73] "ACVRL1" "JAG1" "ANGPT1" "ANGPT2" ...
  ..- attr(*, "spec")=
  .. .. cols(
  .. ..   EnsembleID = col_character(),
  .. ..   GeneName = col_character()
  .. .. )
 $ apoptosis      :'data.frame':    66 obs. of  2 variables:
  ..$ ensembl_gene_id: chr [1:66] "ENSG00000120868" "ENSG00000128272" "ENSG00000149311" "ENSG00000030110" ...
  ..$ symbol         : chr [1:66] "APAF1" "ATF4" "ATM" "BAK1" ...
  ..- attr(*, "spec")=
  .. .. cols(
  .. ..   EnsembleID = col_character(),
  .. ..   GeneName = col_character()
  .. .. )

Each particular pathway or functional gene set contain two column: ensembl_gene_id symbol

CancerSEA$angiogenesis

# A tibble: 73 x 2
   ensembl_gene_id symbol
   <chr>           <chr> 
 1 ENSG00000139567 ACVRL1
 2 ENSG00000101384 JAG1  
 3 ENSG00000154188 ANGPT1
 4 ENSG00000091879 ANGPT2
 5 ENSG00000174059 CD34  
 6 ENSG00000070831 CDC42 
 7 ENSG00000112062 MAPK14
 8 ENSG00000025708 TYMP  
 9 ENSG00000078401 EDN1  
10 ENSG00000125266 EFNB2 
# ... with 63 more rows