MSnID
This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see MSnID.
Utilities for Exploration and Assessment of Confidence of LC-MSn Proteomics Identifications
Bioconductor version: 3.16
Extracts MS/MS ID data from mzIdentML (leveraging mzID package) or text files. After collating the search results from multiple datasets it assesses their identification quality and optimize filtering criteria to achieve the maximum number of identifications while not exceeding a specified false discovery rate. Also contains a number of utilities to explore the MS/MS results and assess missed and irregular enzymatic cleavages, mass measurement accuracy, etc.
Author: Vlad Petyuk with contributions from Laurent Gatto
Maintainer: Vlad Petyuk <petyuk at gmail.com>
citation("MSnID")):
Installation
To install this package, start R (version "4.2") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("MSnID")
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("MSnID")| Handling Modifications with MSnID | R Script | |
| MSnID Package for Handling MS/MS Identifications | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ImmunoOncology, MassSpectrometry, Proteomics, Software |
| Version | 1.32.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (9.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 2.10), Rcpp |
| Imports | MSnbase(>= 1.12.1), mzID(>= 1.3.5), R.cache, foreach, doParallel, parallel, methods, iterators, data.table, Biobase, ProtGenerics, reshape2, dplyr, mzR, BiocStyle, msmsTests, ggplot2, RUnit, BiocGenerics, Biostrings, purrr, rlang, stringr, tibble, AnnotationHub, AnnotationDbi, xtable |
| System Requirements | |
| URL |
See More
| Suggests | |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | RforProteomics |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | MSnID_1.32.0.tar.gz |
| Windows Binary | MSnID_1.32.0.zip (64-bit only) |
| macOS Binary (x86_64) | MSnID_1.32.0.tgz |
| macOS Binary (arm64) | MSnID_1.32.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/MSnID |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MSnID |
| Bioc Package Browser | https://code.bioconductor.org/browse/MSnID/ |
| Package Short Url | https://bioconductor.org/packages/MSnID/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.16 | Source Archive |