Package: RHybridFinder 0.2.0

Frederic Saab

RHybridFinder: Identification of Hybrid Peptides in Immunopeptidomic Analyses

Tool for the analysis Mass Spectrometry (MS) data in the context of immunopeptidomic analysis for the identification of hybrid peptides and the predictions of binding affinity of all peptides using 'netMHCpan' <doi:10.1093/nar/gkaa379> while providing a summary of the netMHCpan output. 'RHybridFinder' (RHF) is destined for researchers who are looking to analyze their MS data for the purpose of identification of potential spliced peptides. This package, developed mainly in base R, is based on the workflow published by Faridi et al. in 2018 <doi:10.1126/sciimmunol.aar3947>.

Authors:Frederic Saab [aut, cre], Peter Kubiniok [aut]

RHybridFinder_0.2.0.tar.gz
RHybridFinder_0.2.0.tar.gz(r-4.5-noble)RHybridFinder_0.2.0.tar.gz(r-4.4-noble)
RHybridFinder_0.2.0.tgz(r-4.4-emscripten)RHybridFinder_0.2.0.tgz(r-4.3-emscripten)
RHybridFinder.pdf |RHybridFinder.html
RHybridFinder/json (API)
NEWS

# Install 'RHybridFinder' in R:
install.packages('RHybridFinder', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.00 score 5 scripts 196 downloads 7 exports 14 dependencies

Last updated 3 years agofrom:3a89236619. Checks:OK: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 01 2024
R-4.5-linuxOKDec 01 2024

Exports:checknetMHCpanexport_checknetmhcpan_resultsexport_HybridFinder_resultsexport_step2_resultsHybridFindermhc_checkstep2_wo_netMHCpan

Dependencies:ade4codetoolsdoParallelforeachiteratorslatticeMASSnlmepixmapRcppRcppArmadillosegmentedseqinrsp

RHybridFinder

Rendered fromRHybridFinder.Rmdusingknitr::rmarkdownon Dec 01 2024.

Last update: 2021-08-17
Started: 2021-06-21

Readme and manuals

Help Manual

Help pageTopics
checknetMHCpanchecknetMHCpan
db_Human_Liver_AUTD17db_Human_Liver_AUTD17
db_rerun_Human_Liver_AUTD17db_rerun_Human_Liver_AUTD17
denovo_Human_Liver_AUTD17denovo_Human_Liver_AUTD17
export_checknetmhcpan_resultsexport_checknetmhcpan_results
export_HybridFinder_resultsexport_HybridFinder_results
export_step2_resultsexport_step2_results
HybridFinderHybridFinder
mhc_checkmhc_check
netmhcpan_list_allelesnetmhcpan_list_alleles
step2_wo_netMHCpanstep2_wo_netMHCpan