pmartR: Panomics Marketplace - Quality Control and Statistical Analysis for Panomics Data

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>.

Version: 2.4.4
Depends: R (≥ 3.5.0)
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
LinkingTo: Rcpp, RcppArmadillo, BH
Suggests: knitr, limma, rmarkdown, edgeR, DESeq2, plotly, scales, S4Vectors, survival, testthat, trelliscopejs, pmartRdata, vdiffr
Published: 2024-02-27
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 at pnnl.gov>
BugReports: https://github.com/pmartR/pmartR/issues
License: BSD_2_clause + file LICENSE
URL: https://pmartr.github.io/pmartR/, https://github.com/pmartR/pmartR
NeedsCompilation: yes
Additional_repositories: https://pmartR.github.io/drat
Citation: pmartR citation info
Materials: README
CRAN checks: pmartR results

Documentation:

Reference manual: pmartR.pdf

Downloads:

Package source: pmartR_2.4.4.tar.gz
Windows binaries: r-devel: pmartR_2.4.4.zip, r-release: pmartR_2.4.4.zip, r-oldrel: pmartR_2.4.4.zip
macOS binaries: r-release (arm64): not available, r-oldrel (arm64): not available, r-release (x86_64): pmartR_2.4.4.tgz
Old sources: pmartR archive

Linking:

Please use the canonical form https://CRAN.R-project.org/package=pmartR to link to this page.