Package: MSnID
Type: Package
Title: Utilities for Exploration and Assessment of Confidence of LC-MSn
        Proteomics Identifications
Version: 1.44.0
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: libglpk-dev make libicu-dev libpng-dev libxml2-dev
        libnetcdf-dev libssl-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 14:21:36 UTC
RemoteUrl: https://github.com/bioc/MSnID
RemoteRef: RELEASE_3_22
RemoteSha: 80a4b14a53d64fd97c0aaa8459a48b6dad18166b
NeedsCompilation: no
Packaged: 2025-11-11 16:08:29 UTC; root
Built: R 4.5.2; ; 2025-11-11 16:25:01 UTC; windows
