RaggedExperiment

DOI: 10.18129/B9.bioc.RaggedExperiment  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see RaggedExperiment.

Representation of Sparse Experiments and Assays Across Samples

Bioconductor version: 3.16

This package provides a flexible representation of copy number, mutation, and other data that fit into the ragged array schema for genomic location data. The basic representation of such data provides a rectangular flat table interface to the user with range information in the rows and samples/specimen in the columns. The RaggedExperiment class derives from a GRangesList representation and provides a semblance of a rectangular dataset.

Author: Martin Morgan [aut], Marcel Ramos [aut, cre]

Maintainer: Marcel Ramos <marcel.ramos at roswellpark.org>

Installation

To install this package, start R (version "4.2") and enter:

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

BiocManager::install("RaggedExperiment")

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("RaggedExperiment")

 

HTML	R Script	RaggedExperiment
PDF		Reference Manual
Text		NEWS

Details

biocViews	DataRepresentation, Infrastructure, Software
Version	1.22.0
In Bioconductor since	BioC 3.5 (R-3.4) (6 years)
License	Artistic-2.0
Depends	R (>= 4.2.0), GenomicRanges(>= 1.37.17)
Imports	BiocGenerics, GenomeInfoDb, IRanges, Matrix, MatrixGenerics, methods, S4Vectors, stats, SummarizedExperiment, utils
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, testthat, MultiAssayExperiment
SystemRequirements
Enhances
URL
BugReports	https://github.com/Bioconductor/RaggedExperiment/issues
Depends On Me	CNVRanger, compartmap
Imports Me	cBioPortalData, omicsPrint, RTCGAToolbox, TCGAutils, terraTCGAdata
Suggests Me	curatedTCGAData, maftools, MultiAssayExperiment, MultiDataSet, SingleCellMultiModal, TENxIO
Links To Me
Build Report

Package Archives

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

Source Package	RaggedExperiment_1.22.0.tar.gz
Windows Binary	RaggedExperiment_1.22.0.zip
macOS Binary (x86_64)	RaggedExperiment_1.22.0.tgz
macOS Binary (arm64)	RaggedExperiment_1.22.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/RaggedExperiment
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/RaggedExperiment
Bioc Package Browser	https://code.bioconductor.org/browse/RaggedExperiment/
Package Short Url	https://bioconductor.org/packages/RaggedExperiment/
Package Downloads Report	Download Stats