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BumpyMatrix

This is the development version of BumpyMatrix; for the stable release version, see BumpyMatrix.

Bumpy Matrix of Non-Scalar Objects


Bioconductor version: Development (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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews DataRepresentation, Infrastructure, Software
Version 1.11.0
In Bioconductor since BioC 3.13 (R-4.1) (3 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
See More
Suggests BiocStyle, knitr, rmarkdown, testthat
Linking To
Enhances
Depends On Me alabaster.bumpy
Imports Me CoreGx, gDRcore, gDRimport, gDRutils, MerfishData, MouseGastrulationData, TENxXeniumData
Suggests Me escheR, gDR, ggspavis, SpatialExperiment, STexampleData
Links To Me
Build Report Build Report

Package Archives

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

Source Package BumpyMatrix_1.11.0.tar.gz
Windows Binary BumpyMatrix_1.11.0.zip
macOS Binary (x86_64) BumpyMatrix_1.11.0.tgz
macOS Binary (arm64) BumpyMatrix_1.11.0.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