(pronounced ipr-scanner)
An R package for accessing InterProScan5 API | for protein scanning & characterization
devtools::install_github("jravilab/iprscanr") or
remotes::install_github("jravilab/iprscanr")
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"
Learn more about the in-dev package here.
How to a build a package? Material from GLBIO 2023
Jacob Krol, Faisal Alquaddoomi, Janani Ravi
*General correspondence should be addressed to JR at janani.ravi@cuanschutz.edu.