RaggedExperiment
This is the released version of RaggedExperiment; for the devel version, see RaggedExperiment.
Representation of Sparse Experiments and Assays Across Samples
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.36.0 |
| In Bioconductor since | BioC 3.5 (R-3.4) (9.5 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/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, 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.
| Source Package | RaggedExperiment_1.36.0.tar.gz |
| Windows Binary (x86_64) | RaggedExperiment_1.36.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | RaggedExperiment_1.36.0.tgz |
| macOS Binary (sonoma-arm64) | RaggedExperiment_1.36.0.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 |