BumpyMatrix

Bumpy Matrix of Non-Scalar Objects

Bioconductor version: Release (3.19)

Implements the BumpyMatrix class and several subclasses for holding non-scalar objects in each entry of the matrix. This is akin to a ragged array but the raggedness is in the third dimension, much like a bumpy surface - hence the name. Of particular interest is the BumpyDataFrameMatrix, where each entry is a Bioconductor data frame. This allows us to naturally represent multivariate data in a format that is compatible with two-dimensional containers like the SummarizedExperiment and MultiAssayExperiment objects.

Author: Aaron Lun [aut, cre], Genentech, Inc. [cph]

Maintainer: Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>

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

Installation

To install this package, start R (version "4.4") and enter:


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

BiocManager::install("BumpyMatrix")

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("BumpyMatrix")

The BumpyMatrix class	HTML	R Script
Reference Manual	PDF
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataRepresentation, Infrastructure, Software
Version	1.12.0
In Bioconductor since	BioC 3.13 (R-4.1) (3.5 years)
License	MIT + file LICENSE
Depends
Imports	utils, methods, Matrix, S4Vectors, IRanges
System Requirements
URL	https://bioconductor.org/packages/BumpyMatrix
Bug Reports	https://github.com/LTLA/BumpyMatrix/issues

Suggests	BiocStyle, knitr, rmarkdown, testthat
Linking To
Enhances
Depends On Me	alabaster.bumpy
Imports Me	CoreGx, gDRcore, gDRimport, gDRutils, MerfishData, MouseGastrulationData, TENxXeniumData
Suggests Me	SpatialExperiment, escheR, gDR, ggspavis, tpSVG, STexampleData
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	BumpyMatrix_1.12.0.tar.gz
Windows Binary (x86_64)	BumpyMatrix_1.12.0.zip
macOS Binary (x86_64)	BumpyMatrix_1.12.0.tgz
macOS Binary (arm64)	BumpyMatrix_1.12.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/BumpyMatrix
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/BumpyMatrix
Bioc Package Browser	https://code.bioconductor.org/browse/BumpyMatrix/
Package Short Url	https://bioconductor.org/packages/BumpyMatrix/
Package Downloads Report	Download Stats