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This is the development version of DIAlignR; for the stable release version, see DIAlignR.

Dynamic Programming Based Alignment of MS2 Chromatograms

Bioconductor version: Development (3.19)

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")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

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


biocViews Alignment, MassSpectrometry, Metabolomics, Proteomics, Software
Version 2.11.0
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
Bug Reports https://github.com/shubham1637/DIAlignR/issues
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Suggests knitr, akima, lattice, scales, gridExtra, latticeExtra, rmarkdown, BiocStyle, BiocParallel, testthat (>= 2.1.0)
Linking To Rcpp, RcppEigen
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Follow Installation instructions to use this package in your R session.

Source Package DIAlignR_2.11.0.tar.gz
Windows Binary DIAlignR_2.11.0.zip
macOS Binary (x86_64) DIAlignR_2.11.0.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/
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