Bioconductor - MSnID

Bioconductor - MSnID
Bioconductor 3.22
Software Packages
MSnID
MSnID
This is the
released
version of MSnID; for the devel version, see
MSnID
Utilities for Exploration and Assessment of Confidence of LC-MSn Proteomics Identifications
DOI:
10.18129/B9.bioc.MSnID
Bioconductor version:
Release (3.22)
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
Citation (from within R, enter
citation("MSnID")
):
Installation
To install this package, start R (version "4.5") 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
PDF
R Script
MSnID Package for Handling MS/MS Identifications
PDF
R Script
Reference Manual
PDF
NEWS
Text
Need some help? Ask on the Bioconductor Support site!
Details
biocViews
ImmunoOncology
MassSpectrometry
Proteomics
Software
Version
1.44.2
In Bioconductor since
BioC 3.0 (R-3.1) (11.5 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_1.44.2.tar.gz
Windows Binary (x86_64)
MSnID_1.44.2.zip
(64-bit only)
macOS Binary (x86_64)
MSnID_1.44.2.tgz
macOS Binary (arm64)
MSnID_1.44.2.tgz
Source Repository
git clone https://git.bioconductor.org/packages/MSnID
Source Repository (Developer Access)
git clone git@git.bioconductor.org:packages/MSnID
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