DIAlignR
This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see DIAlignR.
Dynamic Programming Based Alignment of MS2 Chromatograms
Bioconductor version: 3.14
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("DIAlignR")):
Installation
To install this package, start R (version "4.1") 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 | ||
| NEWS | Text |
Details
| biocViews | Alignment, MassSpectrometry, Metabolomics, Proteomics, Software |
| Version | 2.2.0 |
| 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_2.2.0.tar.gz |
| Windows Binary | DIAlignR_2.2.0.zip (32- & 64-bit) |
| macOS 10.13 (High Sierra) | DIAlignR_2.2.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/DIAlignR |
| Source Repository (Developer Access) | git clone [email protected]:packages/DIAlignR |
| Bioc Package Browser | https://code.bioconductor.org/browse/DIAlignR/ |
| Package Short Url | https://bioconductor.org/packages/DIAlignR/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.14 | Source Archive |