DOI: 10.18129/B9.bioc.DIAlignR  

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

Dynamic Programming Based Alignment of MS2 Chromatograms

Bioconductor version: Development (3.18)

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>

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biocViews Alignment, MassSpectrometry, Metabolomics, Proteomics, Software
Version 2.9.0
In Bioconductor since BioC 3.11 (R-4.0) (3 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
BugReports https://github.com/shubham1637/DIAlignR/issues
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Source Package DIAlignR_2.9.0.tar.gz
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Bioc Package Browser https://code.bioconductor.org/browse/DIAlignR/
Package Short Url https://bioconductor.org/packages/DIAlignR/
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