RaggedExperiment
Representation of Sparse Experiments and Assays Across Samples
Bioconductor version: Release (3.20)
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] , Lydia King [ctb]
Maintainer: Marcel Ramos <marcel.ramos at sph.cuny.edu>
citation("RaggedExperiment")
):
Installation
To install this package, start R (version "4.4") 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")
ASCAT to RaggedExperiment | HTML | R Script |
RaggedExperiment | HTML | R Script |
Reference Manual | ||
NEWS | Text |
Details
biocViews | DataRepresentation, Infrastructure, Software |
Version | 1.30.0 |
In Bioconductor since | BioC 3.5 (R-3.4) (7.5 years) |
License | Artistic-2.0 |
Depends | R (>= 4.2.0), GenomicRanges(>= 1.37.17) |
Imports | BiocBaseUtils, BiocGenerics, GenomeInfoDb, IRanges, Matrix, MatrixGenerics, methods, S4Vectors, stats, SummarizedExperiment, utils |
System Requirements | |
URL | |
Bug Reports | https://github.com/Bioconductor/RaggedExperiment/issues |
See More
Suggests | BiocStyle, knitr, rmarkdown, testthat, MultiAssayExperiment |
Linking To | |
Enhances | |
Depends On Me | CNVRanger, SARC, curatedPCaData |
Imports Me | cBioPortalData, omicsPrint, RTCGAToolbox, TCGAutils, terraTCGAdata, MOCHA |
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.
Source Package | RaggedExperiment_1.30.0.tar.gz |
Windows Binary (x86_64) | RaggedExperiment_1.30.0.zip |
macOS Binary (x86_64) | RaggedExperiment_1.30.0.tgz |
macOS Binary (arm64) | RaggedExperiment_1.29.5.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 |