ExploreModelMatrix

This is the released version of ExploreModelMatrix; for the devel version, see ExploreModelMatrix.

Graphical Exploration of Design Matrices

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DOI: 10.18129/B9.bioc.ExploreModelMatrix

Bioconductor version: Release (3.22)

Given a sample data table and a design formula, ExploreModelMatrix generates an interactive application for exploration of the resulting design matrix. This can be helpful for interpreting model coefficients and constructing appropriate contrasts in (generalized) linear models. Static visualizations can also be generated.

Author: Charlotte Soneson [aut, cre] ORCID iD ORCID: 0000-0003-3833-2169 , Federico Marini [aut] ORCID iD ORCID: 0000-0003-3252-7758 , Michael Love [aut] ORCID iD ORCID: 0000-0001-8401-0545 , Florian Geier [aut] ORCID iD ORCID: 0000-0002-9076-9264 , Michael Stadler [aut] ORCID iD ORCID: 0000-0002-2269-4934

Maintainer: Charlotte Soneson <charlottesoneson at gmail.com>

Citation (from within R, enter citation("ExploreModelMatrix")):

Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("ExploreModelMatrix")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("ExploreModelMatrix")

ExploreModelMatrix HTML R Script

ExploreModelMatrix-deploy HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DifferentialExpression, ExperimentalDesign, Regression, ShinyApps, Software

Version 1.22.0

In Bioconductor since BioC 3.11 (R-4.0) (5.5 years)

License MIT + file LICENSE

Depends

Imports shiny (>= 1.5.0), shinydashboard, DT, cowplot, utils, dplyr, magrittr, tidyr, ggplot2, stats, methods, rintrojs, scales, tibble, MASS, limma, S4Vectors, shinyjs, rlang

System Requirements

URL https://github.com/csoneson/ExploreModelMatrix

Bug Reports https://github.com/csoneson/ExploreModelMatrix/issues

Suggests testthat (>= 2.1.0), knitr, rmarkdown, htmltools, BiocStyle

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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package ExploreModelMatrix_1.22.0.tar.gz

Windows Binary (x86_64) ExploreModelMatrix_1.21.0.zip

macOS Binary (x86_64) ExploreModelMatrix_1.22.0.tgz

macOS Binary (arm64) ExploreModelMatrix_1.22.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/ExploreModelMatrix

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ExploreModelMatrix

Bioc Package Browser https://code.bioconductor.org/browse/ExploreModelMatrix/

Package Short Url https://bioconductor.org/packages/ExploreModelMatrix/

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