This site is a development preview. As such the content and styling may not be final and is subject to change before going into production. To see more information about the redesign click here.

DIAlignR

Dynamic Programming Based Alignment of MS2 Chromatograms

Bioconductor version: Release (3.17)

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 2.8.0
In Bioconductor since BioC 3.11 (R-4.0) (3.5 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
Linking To Rcpp, RcppEigen
Suggests knitr, akima, lattice, scales, gridExtra, latticeExtra, rmarkdown, BiocStyle, BiocParallel, testthat (>= 2.1.0)
System Requirements C++14
Enhances
URL
Bug Reports https://github.com/shubham1637/DIAlignR/issues
See More
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package DIAlignR_2.8.0.tar.gz
Windows Binary DIAlignR_2.8.0.zip
macOS Binary (x86_64) DIAlignR_2.8.0.tgz
macOS Binary (arm64) DIAlignR_2.7.0.tgz
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