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DIAlignR

Dynamic Programming Based Alignment of MS2 Chromatograms


Bioconductor version: Release (3.18)

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 [aut, cre] , Hannes Rost [aut] , Justin Sing [aut]

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

Citation (from within R, enter citation("DIAlignR")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("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")
MS2 chromatograms based alignment of targeted mass-spectrometry runs HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Alignment, MassSpectrometry, Metabolomics, Proteomics, Software
Version 2.10.0
In Bioconductor since BioC 3.11 (R-4.0) (4 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
System Requirements C++14
URL
Bug Reports https://github.com/shubham1637/DIAlignR/issues
See More
Suggests knitr, akima, lattice, scales, gridExtra, latticeExtra, rmarkdown, BiocStyle, BiocParallel, testthat (>= 2.1.0)
Linking To Rcpp, RcppEigen
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package DIAlignR_2.10.0.tar.gz
Windows Binary DIAlignR_2.10.0.zip
macOS Binary (x86_64) DIAlignR_2.10.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/DIAlignR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/DIAlignR
Bioc Package Browser https://code.bioconductor.org/browse/DIAlignR/
Package Short Url https://bioconductor.org/packages/DIAlignR/
Package Downloads Report Download Stats