pepVet
This is the development version of pepVet; to use it, please install the devel version of Bioconductor.
Evaluate Proteolytic Digests for Proteomics Workflows
Bioconductor version: Development (3.24)
Simulates proteolytic digestion, scores the resulting peptides for LC-MS/MS suitability, compares candidate enzymes, and reports digest quality at the protein level. Supports 40 cleaver-compatible enzyme rules, workflow presets, peptide mass and pI calculations, sequence-local cleavage-efficiency annotations, and proteome-aware uniqueness scoring. Evaluates multi-FASTA files in batches with per-protein triage and proteome-level summaries. Exports peptide lists for Skyline and generic downstream tools and prints styled console reports.
Author: Enes K. Ergin [aut, cre] 
Maintainer: Enes K. Ergin <eneskemalergin at gmail.com>
citation("pepVet")):Enes K. Ergin. pepVet: Evaluate Proteolytic Digests for Proteomics Workflows. doi:10.18129/B9.bioc.pepVet, R package version 0.99.1, https://bioconductor.org/packages/pepVet.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("pepVet")For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("pepVet")| Getting Started with pepVet | HTML | R Script |
| pepVet Compared to Other Tools | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | MassSpectrometry, Proteomics, QualityControl, Software |
| Version | 0.99.1 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.5.0) |
| Imports | Biostrings, cleaver, cli, IRanges, rlang, tibble |
| System Requirements | |
| URL | https://github.com/LangeLab/pepVet https://langelab.github.io/pepVet/ |
| Bug Reports | https://github.com/LangeLab/pepVet/issues |
See More
| Suggests | BiocStyle, ggplot2, patchwork, ragg, testthat (>= 3.0.0), withr, knitr, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | pepVet_0.99.1.tar.gz |
| Windows Binary (x86_64) | pepVet_0.99.1.zip |
| macOS Binary (big-sur-x86_64) | pepVet_0.99.1.tgz |
| macOS Binary (sonoma-arm64) | pepVet_0.99.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/pepVet |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/pepVet |
| Package Short Url | https://bioconductor.org/packages/pepVet/ |
| Package Downloads Report | Download Stats |