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
NeedsCompilation: yes
Packaged: 2025-10-22 16:22:02 UTC; rich401
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>
Repository: CRAN
Date/Publication: 2025-10-22 18:30:02 UTC
Built: R 4.6.0; x86_64-w64-mingw32; 2026-04-15 04:05:34 UTC; windows
Archs: x64
