DESCRIPTION

Package: artMS
Type: Package
Title: Analytical R tools for Mass Spectrometry
Version: 1.10.3
Date: 2021-07-14
Authors@R: c(person("David", "Jimenez-Morales", role = c("aut","cre"),
                     email = "biodavidjm@gmail.com",
                     comment = c(ORCID = "0000-0003-4356-6461")),
             person("Alexandre", "Rosa Campos", role = c("aut","ctb"),
                     comment = c(ORCID = "0000-0003-3988-7764")),
             person("John", "Von Dollen", role = c("aut")),
             person("Nevan", "Krogan", role = c("aut"),
             comment = c(ORCID = "0000-0003-4902-337X")),
             person("Danielle", "Swaney", role = c("aut", "ctb"),
                     comment = c(ORCID = "0000-0001-6119-6084")))
Description: artMS provides a set of tools for the analysis of proteomics 
    label-free datasets. It takes as input the MaxQuant search result 
    output (evidence.txt file) and performs quality control, 
    relative quantification using MSstats, downstream analysis 
    and integration. artMS also provides a set of functions to re-format 
    and make it compatible with other analytical tools, including, SAINTq, 
    SAINTexpress, Phosfate, and PHOTON. Check 
    [http://artms.org](http://artms.org) for details.
License: GPL (>= 3) + file LICENSE
URL: http://artms.org
BugReports: https://github.com/biodavidjm/artMS/issues
Depends: R (>= 4.1.0)
Imports:
  AnnotationDbi,
  bit64,
  circlize,
  cluster,
  corrplot,
  data.table,
  dplyr,
  getopt,
  ggdendro,
  ggplot2,
  gplots,
  ggrepel,
  graphics,
  grDevices,
  grid,
  limma,
  MSstats,
  openxlsx,
  org.Hs.eg.db,
  pheatmap,
  plotly,
  plyr,
  RColorBrewer,
  scales,
  seqinr,
  stats,
  stringr,
  tidyr,
  UpSetR,
  utils,
  VennDiagram,
  yaml
Suggests: 
  BiocStyle,
  ComplexHeatmap,
  factoextra,
  FactoMineR,
  gProfileR,
  knitr, 
  PerformanceAnalytics,
  org.Mm.eg.db,
  rmarkdown,
  testthat
Encoding: UTF-8
LazyLoad: yes
LazyData: true
biocViews: Proteomics, 
  DifferentialExpression, 
  BiomedicalInformatics, 
  SystemsBiology, 
  MassSpectrometry, 
  Annotation, 
  QualityControl, 
  GeneSetEnrichment, 
  Clustering,
  Normalization,
  ImmunoOncology,
  MultipleComparison
NeedsCompilation: no
VignetteBuilder: knitr
RoxygenNote: 7.1.1
Roxygen: list(markdown = TRUE)