Package: DIAlignR
Type: Package
Title: Dynamic Programming Based Alignment of MS2 Chromatograms
Version: 2.9.0
Authors@R: c(person(given = "Shubham", family = "Gupta", role = c("aut", "cre"),
           email = "shubham.1637@gmail.com",
           comment = c(ORCID = "0000-0003-3500-8152")),
           person(given = "Hannes", family = "Rost", role = c("aut"),
           email = "hannes.rost@utoronto.ca",
           comment = c(ORCID = "0000-0003-0990-7488")),
           person(given = "Justin", family = "Sing", role = c("aut"),
           email = "justincsing@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: 7.2.1
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: devel
git_last_commit: 56aeba5
git_last_commit_date: 2023-04-25
Date/Publication: 2023-04-26
NeedsCompilation: yes
Packaged: 2023-04-26 22:19:27 UTC; biocbuild
Author: Shubham Gupta [aut, cre] (<https://orcid.org/0000-0003-3500-8152>),
  Hannes Rost [aut] (<https://orcid.org/0000-0003-0990-7488>),
  Justin Sing [aut]
Maintainer: Shubham Gupta <shubham.1637@gmail.com>
Built: R 4.3.0; x86_64-w64-mingw32; 2023-04-27 11:37:44 UTC; windows
Archs: x64
