DESCRIPTION

Type: Package
Package: msdap
Title: Mass Spectrometry Downstream Analysis Pipeline
Description: Analyze label-free proteomics datasets from various sources (MaxQuant, Spectronaut, etc) using a pipeline that facilitates peptide filtering and many algorithms for normalization and statistical analysis. A comprehensive PDF report can be generated that includes many data visualizations and documentation thereof.
URL: https://github.com/ftwkoopmans/msdap
Version: 1.2.2
Authors@R: 
    person(given = "Frank",
           family = "Koopmans",
           role = c("aut", "cre"),
           email = "frank.koopmans@vu.nl",
           comment = c(ORCID = "0000-0002-4973-5732"))
License: GPL-3 + file LICENSE
Depends: 
    R (>= 3.6),
    rlang (>= 0.4.4),
    dplyr (>= 1.0),
    tibble (>= 3.0),
    tidyr (>= 1.1.0),
    ggplot2 (>= 3.2)
Imports: 
    Biobase (>= 2.40),
    bit64 (>= 0.9.7),
    crayon (>= 1.3.4),
    data.table (>= 1.12.1),
    DBI (>= 1.1),
    devtools (>= 2.1),
    openssl (>= 1.0),
    doParallel (>= 1.0.15),
    forcats (>= 0.4),
    foreach (>= 1.4),
    formatR (>= 1.7),
    ggpubr (>= 0.2.3),
    ggrepel (>= 0.8.1),
    patchwork (>= 1.0.0),
    gtools (>= 3.8.1),
    knitr (>= 1.20),
    xtable (>= 1.7),
    limma (>= 3.30),
    lme4 (>= 1.1),
    MASS (>= 7.3),
    Matrix (>= 1.2),
    matrixStats (>= 0.50),
    msEmpiRe,
    MSnbase (>= 2.12.0),
    nloptr (>= 1.2),
    openxlsx (>= 4.1),
    pcaMethods (>= 1.70),
    pdftools (>= 2.1),
    pROC (>= 1.15),
    purrr (>= 0.3),
    colorspace (>= 1.0),
    readr (>= 1.3),
    tidyselect (>= 1.0),
    rmarkdown (>= 1.14),
    RSQLite (>= 2.0),
    scales (>= 1.1),
    stringr (>= 1.4),
    stringi (>= 1.5.3),
    styler (>= 1.3),
    tinytex (>= 0.17),
    viridis (>= 0.5.1),
    iq (>= 1.9),
    vsn (>= 3.50),
    DEqMS (>= 1.4),
    diann (>= 1.0.1),
    missForest (>= 1.4),
    BiocParallel (>= 1.20),
    variancePartition (>= 1.16),
    archive(>= 1.0.1),
    arrow(>= 13.0.0)
Suggests:
    testthat (>= 2.1)
Remotes: 
    bioc::release/Biobase,
    bioc::release/MSnbase,
    bioc::release/limma,
    bioc::release/vsn,
    bioc::release/DEqMS,
    bioc::release/pcaMethods,
    bioc::release/BiocParallel,
    bioc::release/variancePartition,
    github::zimmerlab/MS-EmpiRe,
    github::vdemichev/diann-rpackage
BiocViews:
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
VignetteBuilder: knitr