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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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 (>= 4.6.0) |
| 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 |
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) | |
| macOS Binary (big-sur-x86_64) | pepVet_0.99.1.tgz |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/pepVet |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/pepVet |
| Bioc Package Browser | https://code.bioconductor.org/browse/pepVet/ |
| Package Short Url | https://bioconductor.org/packages/pepVet/ |
| Package Downloads Report | Download Stats |