Methods in Molec Biol/Cancer Bioinfo article
Repo is currently public.
The Rmd should be converted to pdf using rmarkdown::render("bioccb.Rmd")
It seems that a clean machine would need at least 30GB of RAM to compile.
Good latex and pandoc support are required.
You need packages
needed = c("curatedTCGAData", "TCGAutils", "dplyr", "kableExtra", "TCGAutils",
"survival", "GGally", "cBioPortalData", "GenomicRanges", "ggplot2",
"BiocFileCache", "ExperimentHub", "AnnotationHub", "TumourMethData",
"BiocStyle", "ensembldb",
"SpatialFeatureExperiment", "SFEData")
in addition to knitr and rmarkdown.
The first build in a session is slow. Caching might be used later. The slowness comes from grabbing all assays on a few TCGA tumors, and from resolving various hub requests.