Package: DIAlignR
Type: Package
Title: Dynamic Programming Based Alignment of MS2 Chromatograms
Version: 2.0.0
Author: Shubham Gupta <shubham.1637@gmail.com>, Hannes Rost <hannes.rost@utoronto.ca>
Maintainer: Shubham Gupta <shubham.1637@gmail.com>
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++14
git_url: https://git.bioconductor.org/packages/DIAlignR
git_branch: RELEASE_3_13
git_last_commit: fe5d1ad
git_last_commit_date: 2021-05-19
Date/Publication: 2021-05-19
NeedsCompilation: yes
Packaged: 2021-05-19 23:47:06 UTC; biocbuild
Built: R 4.1.0; i386-w64-mingw32; 2021-05-20 07:51:32 UTC; windows
Archs: i386, x64
