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Bioconductor - SummarizedExperiment (development version)

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 (3.22)

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 (from within R, enter citation("SummarizedExperiment")): Installation

To install this package, start R (version "4.5") 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 PDF NEWS Text Details biocViews Annotation, Coverage, Genetics, GenomeAnnotation, Infrastructure, Sequencing, Software Version 1.39.1 In Bioconductor since BioC 3.2 (R-3.2) (9.5 years) License Artistic-2.0 Depends R (>= 4.0.0), methods, MatrixGenerics(>= 1.1.3), GenomicRanges(>= 1.61.1), 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 AffiXcan, 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