BumpyMatrix
This is the development version of BumpyMatrix; for the stable release version, see BumpyMatrix.
Bumpy Matrix of Non-Scalar Objects
Bioconductor version: Development (3.24)
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("BumpyMatrix")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | ||
| LICENSE | Text |
Details
| biocViews | DataRepresentation, Infrastructure, Software |
| Version | 1.21.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (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 |
See More
| Suggests | BiocStyle, knitr, rmarkdown, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | alabaster.bumpy |
| Imports Me | CoreGx, gDRcore, gDRimport, gDRutils, imageFeatureTCGA, MerfishData, MouseGastrulationData, TENxXeniumData |
| Suggests Me | escheR, gDR, ggspavis, SpatialExperiment, 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_1.21.0.tar.gz |
| Windows Binary (x86_64) | BumpyMatrix_1.21.0.zip |
| macOS Binary (big-sur-x86_64) | BumpyMatrix_1.21.0.tgz |
| macOS Binary (sonoma-arm64) | BumpyMatrix_1.21.0.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 |