Remove R script/notebook package installs (Part 1 of N)

analyses/cnv-chrom-plot/gistic_plot.Rmd

@@ -21,11 +21,6 @@ Rscript -e "rmarkdown::render('analyses/cnv-chrom-plot/gistic_plot.Rmd',
 ### Set Up
 
 ```{r}
-if (!("ggbio" %in% installed.packages())) {
-  install.packages("BiocManager")
-  BiocManager::install("ggbio")
-}
-
 # Magrittr pipe
 `%>%` <- dplyr::`%>%`
 ```

analyses/focal-cn-file-preparation/04-prepare-cn-file.R

@@ -20,39 +20,6 @@
 
 #### Set Up --------------------------------------------------------------------
 
-# We require bioconductor
-if (!("BiocManager" %in% installed.packages())) {
-  install.packages("BiocManager")
-}
-
-# Install GenomicRanges
-if (!("GenomicRanges" %in% installed.packages())) {
-  BiocManager::install("GenomicRanges", update = FALSE)
-}
-
-# Install IRanges
-if (!("IRanges" %in% installed.packages())) {
-  BiocManager::install("IRanges", update = FALSE)
-}
-
-# Install annotatr
-if (!("annotatr" %in% installed.packages())) {
-  BiocManager::install("annotatr", update = FALSE)
-}
-
-# hg38 genome annotations
-if (!("TxDb.Hsapiens.UCSC.hg38.knownGene" %in% installed.packages())) {
-  BiocManager::install("TxDb.Hsapiens.UCSC.hg38.knownGene", update = FALSE)
-}
-
-if (!("org.Hs.eg.db" %in% installed.packages())) {
-  BiocManager::install("org.Hs.eg.db", update = FALSE)
-}
-
-if (!("AnnotationDbi" %in% installed.packages())) {
-  BiocManager::install("AnnotationDbi", update = FALSE)
-}
-
 # Get `magrittr` pipe
 `%>%` <- dplyr::`%>%`