limpca
An R package for the linear modeling of high-dimensional designed data based on ASCA/APCA family of methods
Bioconductor version: 3.23 · Package version: 1.8.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
This package has for objectives to provide a method to make Linear Models for high-dimensional designed data. limpca applies a GLM (General Linear Model) version of ASCA and APCA to analyse multivariate sample profiles generated by an experimental design. ASCA/APCA provide powerful visualization tools for multivariate structures in the space of each effect of the statistical model linked to the experimental design and contrarily to MANOVA, it can deal with mutlivariate datasets having more variables than observations. This method can handle unbalanced design.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("limpca")Details
| Maintainer | Manon Martin <manon.martin@uclouvain.be> |
| Author | Bernadette Govaerts [aut, ths], Sebastien Franceschini [ctb], Robin van Oirbeek [ctb], Michel Thiel [aut], Pascal de Tullio [dtc], Manon Martin [aut, cre] (ORCID: <https://orcid.org/0000-0003-4800-0942>), Nadia Benaiche [ctb] |
| License | Artistic-2.0 |
| URL | https://github.com/ManonMartin/limpca, https://manonmartin.github.io/limpca/ |
| Bug Reports | https://github.com/ManonMartin/limpca/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | ExperimentalDesign, GeneExpression, Metabolomics, MultipleComparison, PrincipalComponent, Regression, Software, StatisticalMethod, Visualization |
| Package Short Url | https://bioconductor.org/packages/limpca/ |
Citation
From within R, enter citation("limpca"):
Bernadette Govaerts, Michel Thiel, Manon Martin. limpca: An R package for the linear modeling of high-dimensional designed data based on ASCA/APCA family of methods. doi:10.18129/B9.bioc.limpca, R package version 1.8.0, https://bioconductor.org/packages/limpca.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
- Application of limpca on the Trout transcriptomic dataset.
- Application of limpca on the UCH metabolomics dataset.
- Get started with limpca.
Download
Follow the installation instructions to use this package in your R session.
| Source package | limpca_1.8.0.tar.gz |
| Windows binary (x86_64) | limpca_1.8.0.zip |
| macOS binary (arm64) | limpca_1.8.0.tgz |
| macOS binary (x86_64) | limpca_1.8.0.tgz |
Dependencies
Depends: R (>= 3.5.0)
Imports: ggplot2, stringr, plyr, ggrepel, reshape2, grDevices, graphics, doParallel, parallel, dplyr, tibble, tidyr, ggsci, tidyverse, methods, stats, SummarizedExperiment, S4Vectors
Suggests: BiocStyle, pander, rmarkdown, car, gridExtra, knitr, testthat (>= 3.0.0)