list2venn.pl : convert a list of genelist to venn diagrams

Usage

    perl list2venn.pl list_file.txt
    R --no-save < list_file.R

list file format (tsv)

    list        | genelist file
    ------------|------------------------------------------------
    up_E2       | geneset.DUTERTRE_ESTRADIOL_RESPONSE_24HR_UP.txt
    down_E2     | geneset.DUTERTRE_ESTRADIOL_RESPONSE_24HR_DN.txt
    E2F_targets | geneset.HALLMARK_E2F_TARGETS.txt

Output

R script that generate venn diagrams

Required R packages

gplots https://cran.r-project.org/web/packages/gplots

 install.packages("gplots")

UpSetR https://cran.r-project.org/web/packages/UpSetR/index.html

install.packages("UpSetR")

Vennerable https://github.com/js229/Vennerable

 library(devtools)
 install_github("js229/Vennerable")
 
 # older version 
 # https://r-forge.r-project.org/projects/vennerable/
 # install.packages("Vennerable", repos="http://R-Forge.R-project.org") 
 
 # R version >= 3.5
 if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
 BiocManager::install(c("graph", "RBGL"))      
 
 # R version < 3.5
 #source("http://bioconductor.org/biocLite.R")
 #biocLite("graph")
 #biocLite("RBGL")

Author

David Laperriere dlaperriere@outlook.com