[quality_check] QC specific Dockerfile(s)

AlexsLemonade / compendium-processing

A series of analyses related to refine.bio species compendia

BSD 3-Clause "New" or "Revised" License

0 stars 0 forks source link

[quality_check] QC specific Dockerfile(s) #15

Closed jaclyn-taroni closed 5 years ago

jaclyn-taroni commented 5 years ago

A running list of packages needed! Note that we'll need two because I had to roll back the version of R for Rsamtools at some point. Unless otherwise noted, this list is for the "typical" Dockerfile (pulled from rocker/tidyverse:3.5.1).

ensembldb
ggfortify

jaclyn-taroni commented 5 years ago

For 3.4.4

BiocInstaller::biocLite(c("limma", "rtracklayer", "GenomicRanges", "Rsamtools"),
                        suppressUpdates = TRUE)

jaclyn-taroni commented 5 years ago

rWikiPathways, GSA, org.Dr.eg.db, XML

jaclyn-taroni commented 5 years ago

BiocManager::install("qvalue", update = FALSE)
devtools::install_github('wgmao/PLIER',
                         ref = 'a2d4a2aa343f9ed4b9b945c04326bebd31533d4d',
                         dependencies = TRUE)
install.packages("cowplot")