iprscanR 🔎

(pronounced ipr-scanner)
An R package for accessing InterProScan5 API | for protein scanning & characterization

Installation

devtools::install_github("jravilab/iprscanr") or
remotes::install_github("jravilab/iprscanr")

Usage

library(iprscanr)
# use example data included with package
submit_ipr(path2seq = system.file(file.path("extdata", "ex-in-CAA75348.1.faa"), package = "iprscanr"),
           outfolder = system.file("extdata", package = "iprscanr"),
           email = "jravilab.msu@gmail.com",
           applications = c("PfamA", "Phobius")
)

# print a character vector of all InterProScan applications
> APPL
 [1] "NCBIfam"               "SFLD"                  "Phobius"               "SignalP"               "SignalP_EUK"          
 [6] "SignalP_GRAM_POSITIVE" "SignalP_GRAM_NEGATIVE" "SuperFamily"           "Panther"               "Gene3d"               
[11] "HAMAP"                 "PrositeProfiles"       "PrositePatterns"       "Coils"                 "SMART"                
[16] "CDD"                   "PRINTS"                "PfamA"                 "MobiDBLite"            "PIRSF"                
[21] "TMHMM"                 "AntiFam"               "FunFam"                "PIRSR"

Documentation

Learn more about the in-dev package here.

How to a build a package? Material from GLBIO 2023

License

MIT License

Authors

Jacob Krol, Faisal Alquaddoomi, Janani Ravi

*General correspondence should be addressed to JR at janani.ravi@cuanschutz.edu.