RaggedExperiment
This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see RaggedExperiment.
Representation of Sparse Experiments and Assays Across Samples
Bioconductor version: 3.18
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 roswellpark.org>
citation("RaggedExperiment")):
Installation
To install this package, start R (version "4.3") 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 | 1.26.0 |
| In Bioconductor since | BioC 3.5 (R-3.4) (7 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, compartmap, SARC |
| Imports Me | cBioPortalData, omicsPrint, RTCGAToolbox, TCGAutils, terraTCGAdata |
| Suggests Me | curatedTCGAData, maftools, MultiAssayExperiment, MultiDataSet, SingleCellMultiModal, TENxIO |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | RaggedExperiment_1.26.0.tar.gz |
| Windows Binary | RaggedExperiment_1.26.0.zip |
| macOS Binary (x86_64) | RaggedExperiment_1.26.0.tgz |
| macOS Binary (arm64) | RaggedExperiment_1.26.0.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 |