Package: pmartR
Type: Package
Title: Panomics Marketplace - Quality Control and Statistical Analysis
        for Panomics Data
Version: 2.5.1
Date: 2025-10-21
Authors@R: c(
    person("Lisa", "Bramer", email = "lisa.bramer@pnnl.gov", role = c("aut", "cre")), 
    person("Kelly", "Stratton", email = "kelly.stratton@pnnl.gov", role = c("aut")), 
    person("Daniel", "Claborne", email = "daniel.claborne@pnnl.gov", role = c("aut")), 
    person("Evan", "Glasscock", role = c("ctb")), 
    person("Rachel", "Richardson", role = c("ctb")), 
    person("David", "Degnan", role=c("ctb")),
    person("Evan", "Martin", role=c("ctb"))
    )
Description: Provides functionality for quality control processing and
        statistical analysis of mass spectrometry (MS) omics data, in
        particular proteomic (either at the peptide or the protein
        level), lipidomic, and metabolomic data, as well as RNA-seq
        based count data and nuclear magnetic resonance (NMR) data.
        This includes data transformation, specification of groups that
        are to be compared against each other, filtering of features
        and/or samples, data normalization, data summarization
        (correlation, PCA), and statistical comparisons between defined
        groups.  Implements methods described in: Webb-Robertson et al.
        (2014) <doi:10.1074/mcp.M113.030932>.  Webb-Robertson et al.
        (2011) <doi:10.1002/pmic.201100078>.  Matzke et al. (2011)
        <doi:10.1093/bioinformatics/btr479>.  Matzke et al. (2013)
        <doi:10.1002/pmic.201200269>.  Polpitiya et al. (2008)
        <doi:10.1093/bioinformatics/btn217>.  Webb-Robertson et al.
        (2010) <doi:10.1021/pr1005247>.
License: BSD_2_clause + file LICENSE
Depends: R (>= 4.1.0),
URL: https://pmartr.github.io/pmartR/, https://github.com/pmartR/pmartR
BugReports: https://github.com/pmartR/pmartR/issues
LinkingTo: Rcpp, RcppArmadillo, BH
biocViews:
Imports: Rcpp (>= 0.12.8), data.table, doParallel, dplyr, ggplot2,
        e1071, foreach, methods, mvtnorm, pcaMethods, purrr, rrcov,
        stringr, tidyr (>= 1.3.0), RColorBrewer, magrittr, parallelly,
        patchwork, glmpca,
Suggests: knitr, limma, rmarkdown, edgeR, DESeq2, plotly, scales,
        S4Vectors, survival, testthat, trelliscopejs, pmartRdata,
        vdiffr
Additional_repositories: https://pmartR.github.io/drat
RoxygenNote: 7.3.2
Encoding: UTF-8
Config/pak/sysreqs: libicu-dev
Repository: https://pmartr.r-universe.dev
Date/Publication: 2025-10-21 19:33:44 UTC
RemoteUrl: https://github.com/pmartr/pmartr
RemoteRef: HEAD
RemoteSha: e46f2f0297939ad8cbe74a4f0df88ae535b8de0b
NeedsCompilation: yes
Packaged: 2026-07-18 06:21:56 UTC; root
Author: Lisa Bramer [aut, cre],
  Kelly Stratton [aut],
  Daniel Claborne [aut],
  Evan Glasscock [ctb],
  Rachel Richardson [ctb],
  David Degnan [ctb],
  Evan Martin [ctb]
Maintainer: Lisa Bramer <lisa.bramer@pnnl.gov>