SummarizedExperiment
This is the development version of SummarizedExperiment; for the stable release version, see SummarizedExperiment.
A container (S4 class) for matrix-like assays
Bioconductor version: Development (3.23)
The SummarizedExperiment container contains one or more assays, each represented by a matrix-like object of numeric or other mode. The rows typically represent genomic ranges of interest and the columns represent samples.
Author: Martin Morgan [aut], Valerie Obenchain [aut], Jim Hester [aut], Hervé Pagès [aut, cre]
Maintainer: Hervé Pagès <hpages.on.github at gmail.com>
citation("SummarizedExperiment")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("SummarizedExperiment")
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("SummarizedExperiment")| 1. SummarizedExperiment for Coordinating Experimental Assays, Samples, and Regions of Interest | HTML | R Script |
| 2. Extending the SummarizedExperiment class | HTML | R Script |
| Reference Manual |
Details
| biocViews | Annotation, Coverage, Genetics, GenomeAnnotation, Infrastructure, Sequencing, Software |
| Version | 1.41.0 |
| In Bioconductor since | BioC 3.2 (R-3.2) (10 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.0.0), methods, MatrixGenerics(>= 1.1.3), GenomicRanges(>= 1.61.4), Biobase |
| Imports | utils, stats, tools, Matrix, BiocGenerics(>= 0.51.3), S4Vectors(>= 0.33.7), IRanges(>= 2.23.9), Seqinfo, S4Arrays(>= 1.1.1), DelayedArray(>= 0.31.12) |
| System Requirements | |
| URL | https://bioconductor.org/packages/SummarizedExperiment |
| Bug Reports | https://github.com/Bioconductor/SummarizedExperiment/issues |
See More
| Suggests | GenomeInfoDb(>= 1.45.5), rhdf5, HDF5Array(>= 1.7.5), annotate, AnnotationDbi, GenomicFeatures, SparseArray, SingleCellExperiment, TxDb.Hsapiens.UCSC.hg19.knownGene, hgu95av2.db, airway(>= 1.15.1), BiocStyle, knitr, rmarkdown, RUnit, testthat, digest |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | SummarizedExperiment_1.41.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/SummarizedExperiment |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SummarizedExperiment |
| Bioc Package Browser | https://code.bioconductor.org/browse/SummarizedExperiment/ |
| Package Short Url | https://bioconductor.org/packages/SummarizedExperiment/ |
| Package Downloads Report | Download Stats |