This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see DIAlignR.
Bioconductor version: 3.12
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 <shubham.1637 at gmail.com>, Hannes Rost <hannes.rost at utoronto.ca>
Maintainer: Shubham Gupta <shubham.1637 at gmail.com>
Citation (from within R,
enter citation("DIAlignR")
):
To install this package, start R (version "4.0") and enter:
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("DIAlignR")
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:
browseVignettes("DIAlignR")
HTML | R Script | MS2 chromatograms based alignment of targeted mass-spectrometry runs |
Reference Manual | ||
Text | NEWS |
biocViews | Alignment, MassSpectrometry, Metabolomics, Proteomics, Software |
Version | 1.2.0 |
In Bioconductor since | BioC 3.11 (R-4.0) (1 year) |
License | GPL-3 |
Depends | methods, stats |
Imports | zoo (>= 1.8-3), dplyr, tidyr, rlang, mzR(>= 2.18), signal, ggplot2, scales, gridExtra, RSQLite, DBI, Rcpp |
LinkingTo | Rcpp |
Suggests | knitr, lattice, latticeExtra, rmarkdown, BiocStyle, testthat (>= 2.1.0) |
SystemRequirements | C++11 |
Enhances | |
URL | |
BugReports | https://github.com/shubham1637/DIAlignR/issues |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | DIAlignR_1.2.0.tar.gz |
Windows Binary | DIAlignR_1.2.0.zip (32- & 64-bit) |
macOS 10.13 (High Sierra) | DIAlignR_1.2.0.tgz |
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 |
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