DIAlignR

DOI: 10.18129/B9.bioc.DIAlignR    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see DIAlignR.

Dynamic Programming Based Alignment of MS2 Chromatograms

Bioconductor version: 3.13

To obtain unbiased proteome coverage from a biological sample, mass-spectrometer is operated in Data Independent Acquisition (DIA) mode. Alignment of these DIA runs establishes consistency and less missing values in complete data-matrix. This package implements dynamic programming with affine gap penalty based approach for pair-wise alignment of analytes. A hybrid approach of global alignment (through MS2 features) and local alignment (with MS2 chromatograms) is implemented in this tool.

Author: Shubham Gupta <shubham.1637 at gmail.com>, Hannes Rost <hannes.rost at utoronto.ca>

Maintainer: Shubham Gupta <shubham.1637 at gmail.com>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("DIAlignR")

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("DIAlignR")

 

HTML	R Script	MS2 chromatograms based alignment of targeted mass-spectrometry runs
PDF		Reference Manual
Text		NEWS

Details

biocViews	Alignment, MassSpectrometry, Metabolomics, Proteomics, Software
Version	2.0.0
In Bioconductor since	BioC 3.11 (R-4.0) (1.5 years)
License	GPL-3
Depends	methods, stats, R (>= 4.0)
Imports	zoo (>= 1.8-3), data.table, magrittr, dplyr, tidyr, rlang, mzR(>= 2.18), signal, bit64, reticulate, ggplot2, RSQLite, DBI, ape, phangorn, pracma, RMSNumpress, Rcpp
LinkingTo	Rcpp, RcppEigen
Suggests	knitr, akima, lattice, scales, gridExtra, latticeExtra, rmarkdown, BiocStyle, BiocParallel, testthat (>= 2.1.0)
SystemRequirements	C++14
Enhances
URL
BugReports	https://github.com/shubham1637/DIAlignR/issues
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Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	DIAlignR_2.0.0.tar.gz
Windows Binary	DIAlignR_2.0.0.zip
macOS 10.13 (High Sierra)	DIAlignR_2.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/DIAlignR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/DIAlignR
Package Short Url	https://bioconductor.org/packages/DIAlignR/
Package Downloads Report	Download Stats