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RaggedExperiment
This is thereleased version of RaggedExperiment; for the devel version, seeRaggedExperiment.
Representation of Sparse Experiments and Assays Across Samples
Bioconductor version: Release (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("RaggedExperiment")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("RaggedExperiment")For older versions of R, please refer to the appropriateBioconductor 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 | 1.34.0 |
| In Bioconductor since | BioC 3.5 (R-3.4) (8.5 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/RaggedExperimenthttps://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,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
FollowInstallation instructions to use this package in your R session.
| Source Package | RaggedExperiment_1.34.0.tar.gz |
| Windows Binary (x86_64) | RaggedExperiment_1.34.0.zip (64-bit only) |
| macOS Binary (x86_64) | RaggedExperiment_1.34.0.tgz |
| macOS Binary (arm64) | RaggedExperiment_1.34.0.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 |