phipmake

R package of Drake-based tools for the Larman Lab’s PhIP-Seq data analysis pipeline.

if(!requireNamespace("remotes")) install.packages("remotes")
remotes::install_github("ropensci/drake") # drake is on CRAN, but phipmake depends on the more recently updated Github version.
remotes::install_github("brandonsie/phipmake")

drake::expose_imports(phipmake) # allow drake to keep track of nested function dependencies.
plan <- phipdrake::define_plan() # initialize pipeline. looks for mpath.txt and ppath.txt in working directory
drake::make(plan) # execute pipeline
v <- drake::vis_drake_graph(drake::drake_config(plan)) # visualize pipeline dependencies
v
visNetwork::visSave(v, "dependency_graph.html") # save dependency graph

Dependency Graph

A simplified version of the dependency graph is below. For a more complete & interactive representation, please click here.

More documentation will come soon to phipmake’s website.

Acknowledgements

• Daniel Monaco wrote the network filter used for polyclonal scoring, and AVARDA, used for deconvoluting viral proteome antibody specificitity data.