RaggedExperiment

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see RaggedExperiment.

Representation of Sparse Experiments and Assays Across Samples

Bioconductor version: 3.13

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.

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

Maintainer: Martin Morgan <martin.morgan at roswellpark.org>

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

Installation

To install this package, start R (version "4.1") 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")

RaggedExperiment HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DataRepresentation, Infrastructure, Software

Version 1.16.0

In Bioconductor since BioC 3.5 (R-3.4) (7 years)

License Artistic-2.0

Depends R (>= 3.6.0), GenomicRanges(>= 1.37.17)

Imports BiocGenerics, GenomeInfoDb, IRanges, Matrix, MatrixGenerics, methods, S4Vectors, stats, SummarizedExperiment

System Requirements

URL

Bug Reports https://github.com/Bioconductor/RaggedExperiment/issues

Suggests BiocStyle, knitr, rmarkdown, testthat, MultiAssayExperiment

Linking To

Enhances

Depends On Me CNVRanger, compartmap

Imports Me cBioPortalData, omicsPrint, RTCGAToolbox, TCGAutils

Suggests Me curatedTCGAData, maftools, MultiAssayExperiment, MultiDataSet, SingleCellMultiModal

Links To Me

Build Report Build Report

Package Archives

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

Source Package RaggedExperiment_1.16.0.tar.gz

Windows Binary RaggedExperiment_1.16.0.zip

macOS 10.13 (High Sierra) RaggedExperiment_1.16.0.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

Old Source Packages for BioC 3.13 Source Archive