MSnID
This is the development version of MSnID; for the stable release version, see MSnID.
Utilities for Exploration and Assessment of Confidence of LC-MSn Proteomics Identifications
Bioconductor version: Development (3.20)
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 "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("MSnID")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual |
Details
| biocViews | ImmunoOncology, MassSpectrometry, Proteomics, Software |
| Version | 1.39.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (10 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 |
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| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/MSnID |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MSnID |
| Package Short Url | https://bioconductor.org/packages/MSnID/ |
| Package Downloads Report | Download Stats |