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
git_url: https://git.bioconductor.org/packages/MSnID
git_branch: RELEASE_3_22
git_last_commit: 80a4b14
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.22
Date/Publication: 2025-10-29
NeedsCompilation: no
Packaged: 2025-10-30 05:19:09 UTC; biocbuild
