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DESCRIPTION
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DESCRIPTION
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Package: DIAlignR
Type: Package
Title: Dynamic Programming Based Alignment of MS2 Chromatograms
Version: 1.3.18
Author: Shubham Gupta <[email protected]>, Hannes Rost <[email protected]>
Maintainer: Shubham Gupta <[email protected]>
Description: 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.
License: GPL-3
Encoding: UTF-8
LazyData: false
RoxygenNote: 7.1.1
biocViews: MassSpectrometry, Metabolomics, Proteomics, Alignment, Software
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
Suggests:
knitr, akima,
lattice, scales, gridExtra,
latticeExtra,
rmarkdown,
BiocStyle, BiocParallel,
testthat (>= 2.1.0)
VignetteBuilder: knitr
BugReports: https://github.com/shubham1637/DIAlignR/issues
LinkingTo:
Rcpp, RcppEigen
SystemRequirements: C++11