R package to build case-control reports from PhIP-Seq data. phipcc depends on multiple other packages including drake, phipmake, epitopefindr. Familiarity with these packages will be useful in working with phipcc.

Setup

  1. In R console, execute:
if(!requireNamespace("remotes")) install.packages("remotes")
remotes::install_github("ropensci/drake")
remotes::install_github("brandonsie/phipmake")
remotes::install_github("brandonsie/epitopefindr")
remotes::install_github("brandonsie/phipcc")

Additional epitopefindr-specific setup steps

  1. Install a TeX distribution with pdflatex. (e.g. MiKTeX (version 2.9+)). (Optional; used to convert multiple sequence alignment TeX files to PDF.)
  2. Install pdftk (version 2.02+). (Optional; used to merge individual PDFs into a single file.)
  3. In R console, execute:
if (!requireNamespace("BiocManager")) install.packages("BiocManager")
BiocManager::install(c("Biostrings", "IRanges", "msa", "S4Vectors"))
remotes::install_github("mhahsler/rBLAST")