Loading the package | Example data | Step 1 | HybridFinder | Description | Loading data | Run HybridFinder | Output | Ouput 1: HybridFinder Step1 output (HF_step1_output) | Ouput 2: List of step1 candidate hybrid peptides | Ouput 3: merged proteome | Export | Interim external step: Second database search using the merged proteome | Step2 | checknetMHCpan | Run checknetMHCpan | Ouput 1: netMHCpan results in long format | Ouput 2: netMHCpan results in wide format | Ouput 3: Database search results updated | step2_wo_netMHCpan | Run step2_wo_netMHCpan | Ouput 1: netMHCpan-ready input | Ouput 2: Database search results updated | References
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:
RHybridFinder_0.2.0.tar.gz
RHybridFinder_0.2.0.tar.gz(r-4.7-any)RHybridFinder_0.2.0.tar.gz(r-4.6-any)
RHybridFinder_0.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
RHybridFinder/json (API)
| # Install 'RHybridFinder' in R: |
| install.packages('RHybridFinder', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- db_Human_Liver_AUTD17 - Db_Human_Liver_AUTD17
- db_rerun_Human_Liver_AUTD17 - Db_rerun_Human_Liver_AUTD17
- denovo_Human_Liver_AUTD17 - Denovo_Human_Liver_AUTD17
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:3a89236619. Checks:4 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 134 | ||
| source / vignettes | OK | 206 | ||
| linux-release-x86_64 | OK | 140 | ||
| wasm-release | OK | 134 |
Exports:checknetMHCpanexport_checknetmhcpan_resultsexport_HybridFinder_resultsexport_step2_resultsHybridFindermhc_checkstep2_wo_netMHCpan
Dependencies:ade4codetoolsdoParallelforeachiteratorslatticeMASSnlmepixmapRcppRcppArmadillosegmentedseqinrsp
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| checknetMHCpan | checknetMHCpan |
| db_Human_Liver_AUTD17 | db_Human_Liver_AUTD17 |
| db_rerun_Human_Liver_AUTD17 | db_rerun_Human_Liver_AUTD17 |
| denovo_Human_Liver_AUTD17 | denovo_Human_Liver_AUTD17 |
| export_checknetmhcpan_results | export_checknetmhcpan_results |
| export_HybridFinder_results | export_HybridFinder_results |
| export_step2_results | export_step2_results |
| HybridFinder | HybridFinder |
| mhc_check | mhc_check |
| netmhcpan_list_alleles | netmhcpan_list_alleles |
| step2_wo_netMHCpan | step2_wo_netMHCpan |