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Bioconductor - RaggedExperiment (development version)

RaggedExperiment

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

Representation of Sparse Experiments and Assays Across Samples

Bioconductor version: Development (3.22)

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] ORCID: 0000-0002-3242-0582 , Lydia King [ctb]

Maintainer: Marcel Ramos <marcel.ramos at sph.cuny.edu>

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

To install this package, start R (version "4.5") and enter:


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

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

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")
Details biocViews DataRepresentation, Infrastructure, Software Version 1.33.7 In Bioconductor since BioC 3.5 (R-3.4) (8 years) License Artistic-2.0 Depends R (>= 4.5.0), GenomicRanges(>= 1.61.1) Imports BiocBaseUtils, BiocGenerics, Seqinfo, IRanges, Matrix, MatrixGenerics, methods, S4Vectors, stats, SummarizedExperiment(>= 1.39.1), utils System Requirements URL https://bioconductor.github.io/RaggedExperiment https://bioconductor.org/packages/RaggedExperiment Bug Reports https://github.com/Bioconductor/RaggedExperiment/issues See More Suggests BiocStyle, knitr, rmarkdown, testthat, GenomeInfoDb, MultiAssayExperiment Linking To Enhances Depends On Me CNVRanger, SARC, curatedPCaData Imports Me cBioPortalData, omicsPrint, RTCGAToolbox, TCGAutils, terraTCGAdata Suggests Me maftools, MultiAssayExperiment, MultiDataSet, TENxIO, curatedTCGAData, SingleCellMultiModal Links To Me Build Report Build Report Package Archives

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

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