SummarizedExperiment: SummarizedExperiment container

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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, Valerie Obenchain, Jim Hester, Hervé Pagès
Date of publication
None
Maintainer
Bioconductor Package Maintainer <maintainer@bioconductor.org>
License
Artistic-2.0
Version
1.4.0

View on Bioconductor

Man pages

Assays-class
Assays objects
coverage-methods
Coverage of a RangedSummarizedExperiment object
findOverlaps-methods
Finding overlapping ranges in RangedSummarizedExperiment...
inter-range-methods
Inter range transformations of a RangedSummarizedExperiment...
intra-range-methods
Intra range transformations of a RangedSummarizedExperiment...
makeSummarizedExperimentFromDataFrame
Make a RangedSummarizedExperiment from a data.frame or...
makeSummarizedExperimentFromExpressionSet
Make a RangedSummarizedExperiment object from an...
nearest-methods
Finding the nearest range neighbor in...
RangedSummarizedExperiment-class
RangedSummarizedExperiment objects
readKallisto
Input kallisto or kallisto bootstrap results.
SummarizedExperiment-class
SummarizedExperiment objects

Files in this package

SummarizedExperiment/DESCRIPTION
SummarizedExperiment/NAMESPACE
SummarizedExperiment/NEWS
SummarizedExperiment/R
SummarizedExperiment/R/Assays-class.R
SummarizedExperiment/R/RangedSummarizedExperiment-class.R
SummarizedExperiment/R/SummarizedExperiment-class.R
SummarizedExperiment/R/coverage-methods.R
SummarizedExperiment/R/findOverlaps-methods.R
SummarizedExperiment/R/inter-range-methods.R
SummarizedExperiment/R/intra-range-methods.R
SummarizedExperiment/R/makeSummarizedExperimentFromDataFrame.R
SummarizedExperiment/R/makeSummarizedExperimentFromExpressionSet.R
SummarizedExperiment/R/nearest-methods.R
SummarizedExperiment/R/readKallisto.R
SummarizedExperiment/R/zzz.R
SummarizedExperiment/TODO
SummarizedExperiment/build
SummarizedExperiment/build/vignette.rds
SummarizedExperiment/inst
SummarizedExperiment/inst/doc
SummarizedExperiment/inst/doc/SummarizedExperiment.R
SummarizedExperiment/inst/doc/SummarizedExperiment.Rmd
SummarizedExperiment/inst/doc/SummarizedExperiment.html
SummarizedExperiment/inst/extdata
SummarizedExperiment/inst/extdata/kallisto
SummarizedExperiment/inst/extdata/kallisto/abundance.h5
SummarizedExperiment/inst/extdata/kallisto/abundance.tsv
SummarizedExperiment/inst/extdata/kallisto/abundance.txt
SummarizedExperiment/inst/extdata/kallisto/run_info.json
SummarizedExperiment/inst/scripts
SummarizedExperiment/inst/scripts/Find_and_update_objects
SummarizedExperiment/inst/scripts/Find_and_update_objects/README
SummarizedExperiment/inst/scripts/Find_and_update_objects/collect_rda_objects_to_update.R
SummarizedExperiment/inst/scripts/Find_and_update_objects/data_store_RDA_OBJECTS_TO_UPDATE
SummarizedExperiment/inst/scripts/Find_and_update_objects/pkgs_RDA_OBJECTS_TO_UPDATE
SummarizedExperiment/inst/scripts/Find_and_update_objects/scan_rda_files.R
SummarizedExperiment/inst/scripts/Find_and_update_objects/update_rda_objects.R
SummarizedExperiment/inst/unitTests
SummarizedExperiment/inst/unitTests/test_Assays-class.R
SummarizedExperiment/inst/unitTests/test_RangedSummarizedExperiment-class.R
SummarizedExperiment/inst/unitTests/test_SummarizedExperiment-class.R
SummarizedExperiment/inst/unitTests/test_coverage-methods.R
SummarizedExperiment/inst/unitTests/test_findOverlaps-methods.R
SummarizedExperiment/inst/unitTests/test_inter-range-methods.R
SummarizedExperiment/inst/unitTests/test_intra-range-methods.R
SummarizedExperiment/inst/unitTests/test_makeSummarizedExperimentFromDataFrame.R
SummarizedExperiment/inst/unitTests/test_makeSummarizedExperimentFromExpressionSet.R
SummarizedExperiment/inst/unitTests/test_nearest-methods.R
SummarizedExperiment/man
SummarizedExperiment/man/Assays-class.Rd
SummarizedExperiment/man/RangedSummarizedExperiment-class.Rd
SummarizedExperiment/man/SummarizedExperiment-class.Rd
SummarizedExperiment/man/coverage-methods.Rd
SummarizedExperiment/man/findOverlaps-methods.Rd
SummarizedExperiment/man/inter-range-methods.Rd
SummarizedExperiment/man/intra-range-methods.Rd
SummarizedExperiment/man/makeSummarizedExperimentFromDataFrame.Rd
SummarizedExperiment/man/makeSummarizedExperimentFromExpressionSet.Rd
SummarizedExperiment/man/nearest-methods.Rd
SummarizedExperiment/man/readKallisto.Rd
SummarizedExperiment/tests
SummarizedExperiment/tests/run_unitTests.R
SummarizedExperiment/vignettes
SummarizedExperiment/vignettes/SummarizedExperiment.Rmd