Package: MSnID
Type: Package
Title: Utilities for Exploration and Assessment of Confidence of LC-MSn
        Proteomics Identifications
Version: 1.46.0
Author: Vlad Petyuk with contributions from Laurent Gatto
Maintainer: Vlad Petyuk <petyuk@gmail.com>
Description: 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.
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
Suggests:
LazyData: yes
biocViews: Proteomics, MassSpectrometry, ImmunoOncology
Config/pak/sysreqs: cmake libglpk-dev make libicu-dev libpng-dev
        libuv1-dev libxml2-dev libnetcdf-dev libssl-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2026-04-28 12:39:47 UTC
RemoteUrl: https://github.com/bioc/MSnID
RemoteRef: RELEASE_3_23
RemoteSha: b92ae22af69abaa2679e4b7e5b9f4dc7fab78ce3
NeedsCompilation: no
Packaged: 2026-04-29 23:30:33 UTC; root
Built: R 4.6.0; ; 2026-04-29 23:36:14 UTC; windows
