DIAlignR

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

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

Dynamic Programming Based Alignment of MS2 Chromatograms

Bioconductor version: Development (3.21)

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] (ORCID: ), Hannes Rost [aut] (ORCID: ), 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 "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("DIAlignR")

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

Documentation


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Alignment, MassSpectrometry, Metabolomics, Proteomics, Software
Version	2.15.1
In Bioconductor since	BioC 3.11 (R-4.0) (4.5 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
System Requirements	C++14
URL
Bug Reports	https://github.com/shubham1637/DIAlignR/issues

Suggests	knitr, akima, lattice, scales, gridExtra, latticeExtra, rmarkdown, BiocStyle, BiocParallel, testthat (>= 2.1.0)
Linking To	Rcpp, RcppEigen
Enhances
Depends On Me
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Build Report	Build Report

Package Archives

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

Source Package
Windows Binary (x86_64)
macOS Binary (x86_64)
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
Package Short Url	https://bioconductor.org/packages/DIAlignR/
Package Downloads Report	Download Stats