easyRNASeq: Count summarization and normalization for RNA-Seq data

Calculates the coverage of high-throughput short-reads against a genome of reference and summarizes it per feature of interest (e.g. exon, gene, transcript). The data can be normalized as 'RPKM' or by the 'DESeq' or 'edgeR' package.

AuthorNicolas Delhomme, Ismael Padioleau, Bastian Schiffthaler, Niklas Maehler
Date of publicationNone
MaintainerNicolas Delhomme <nicolas.delhomme@umu.se>
LicenseArtistic-2.0
Version2.10.0

View on Bioconductor

Man pages

basename-methods: Extend the basename function to display Rsamtools BamFile...

DESeq-methods: Extension for the DESeq package

easyRNASeq-accessors: Accessors for RNAseq class

easyRNASeq-annotation-internal-methods: Internal easyRNASeq annotation methods

easyRNASeq-annotation-methods: Get genic annotation from a gff3/gtf file or using biomaRt

easyRNASeq-AnnotParam: AnnotParam constructor

easyRNASeq-AnnotParam-accessors: Accessors for AnnotParam class

easyRNASeq-AnnotParam-class: Class "AnnotParam"

easyRNASeq-BamFileList: Get a BamFileList from a list of filenames

easyRNASeq-BamParam: BamParam constructor

easyRNASeq-BamParam-accessors: Accessors for BamParam class

easyRNASeq-BamParam-class: Class "BamParam"

easyRNASeq-class: Class "RNAseq"

easyRNASeq-correction-methods: easyRNASeq count table correction to RPKM

easyRNASeq-coverage-methods: Compute the coverage from a Short Read Alignment file

easyRNASeq-datasets: Dataset included in the package

easyRNASeq-defunct: The following function are defunct: • 'fetchAnnotation' •...

easyRNASeq-defunct-annotation-methods: Defunct annotation function

easyRNASeq-deprecated: The following function have been deprecated: • 'easyRNASeq' •...

easyRNASeq-easyRNASeq: easyRNASeq method

easyRNASeq-global-variables: Objects created when the package is attached.

easyRNASeq-internal-AnnotParam-methods: Internal methods of AnnotParam objects

easyRNASeq-internal-methods: Internal methods of RNAseq objects

easyRNASeq-island-methods: Identify expressed regions de-novo

easyRNASeq-package: Count summarization and normalization pipeline for Next...

easyRNASeq-RnaSeqParam: RnaSeqParam constructor

easyRNASeq-RnaSeqParam-accessors: Accessors for RnaSeqParam class

easyRNASeq-RnaSeqParam-class: Class "RnaSeqParam"

easyRNASeq-simpleRNASeq: simpleRNASeq method

easyRNASeq-summarization-internal-methods: Internal count and summarization methods

easyRNASeq-summarization-methods: Count methods for RNAseq object

easyRNASeq-synthetic-transcripts: Methods to create synthetic transcripts

edgeR-methods: Extension for the edgeR package

file.exists-methods: Extend the file.exists function to check the path slot of a...

genomeIntervals-methods: Extension for the genomeIntervals package

GenomicRanges-methods: Extension of the GenomicRanges package

IRanges-methods: Extension of the IRanges package

parallel-methods: parallel additional methods

print-methods: Pretty print the content of classes from the easyRNASeq...

Rsamtools-methods: Extension of the Rsamtools package

ShortRead-methods: Methods extending the ShortRead package functionalities

show-methods: Display the content of classes from the easyRNASeq package.

Files in this package

easyRNASeq/DESCRIPTION
easyRNASeq/NAMESPACE
easyRNASeq/NEWS
easyRNASeq/R
easyRNASeq/R/AllClasses.R easyRNASeq/R/AllGenerics.R easyRNASeq/R/DESeq-methods.R easyRNASeq/R/GenomicRanges-methods.R easyRNASeq/R/IRanges-methods.R easyRNASeq/R/Rsamtools-methods.R easyRNASeq/R/ShortRead-methods.R easyRNASeq/R/basename-methods.R easyRNASeq/R/easyRNASeq-AnnotParam-accessors.R easyRNASeq/R/easyRNASeq-AnnotParam.R easyRNASeq/R/easyRNASeq-BamFileList.R easyRNASeq/R/easyRNASeq-BamParam-accessors.R easyRNASeq/R/easyRNASeq-BamParam.R easyRNASeq/R/easyRNASeq-RnaSeqParam-accessors.R easyRNASeq/R/easyRNASeq-RnaSeqParam.R easyRNASeq/R/easyRNASeq-accessors.R easyRNASeq/R/easyRNASeq-annotation.R easyRNASeq/R/easyRNASeq-counts.R easyRNASeq/R/easyRNASeq-coverage-methods.R easyRNASeq/R/easyRNASeq-internal-AnnotParam-methods.R easyRNASeq/R/easyRNASeq-internal-annotation.R easyRNASeq/R/easyRNASeq-internal-counts.R easyRNASeq/R/easyRNASeq-internal-methods.R easyRNASeq/R/easyRNASeq-internal-normalize.R easyRNASeq/R/easyRNASeq-islands.R easyRNASeq/R/easyRNASeq-methods.R easyRNASeq/R/easyRNASeq-normalize.R easyRNASeq/R/easyRNASeq-package.R easyRNASeq/R/easyRNASeq-simpleRNASeq.R easyRNASeq/R/easyRNASeq-synthetic-transcripts.R easyRNASeq/R/edgeR-methods.R easyRNASeq/R/file.exists-methods.R easyRNASeq/R/genomeIntervals-methods.R easyRNASeq/R/parallel-methods.R easyRNASeq/R/print-methods.R easyRNASeq/R/show-methods.R
easyRNASeq/build
easyRNASeq/build/vignette.rds
easyRNASeq/data
easyRNASeq/data/RobinsonDelhomme2014.txt.gz
easyRNASeq/inst
easyRNASeq/inst/CITATION
easyRNASeq/inst/doc
easyRNASeq/inst/doc/easyRNASeq.R
easyRNASeq/inst/doc/easyRNASeq.Rnw
easyRNASeq/inst/doc/easyRNASeq.pdf
easyRNASeq/inst/doc/simpleRNASeq.R
easyRNASeq/inst/doc/simpleRNASeq.Rmd
easyRNASeq/inst/doc/simpleRNASeq.html
easyRNASeq/inst/unitTests
easyRNASeq/inst/unitTests/test_accessors.R
easyRNASeq/inst/unitTests/test_annotations.R
easyRNASeq/inst/unitTests/test_classes.R
easyRNASeq/inst/unitTests/test_extensions.R
easyRNASeq/inst/unitTests/test_methods.R
easyRNASeq/inst/unitTests/test_print.R
easyRNASeq/inst/unitTests/test_ranges.R
easyRNASeq/inst/unitTests/test_variables.R
easyRNASeq/man
easyRNASeq/man/DESeq-methods.Rd easyRNASeq/man/GenomicRanges-methods.Rd easyRNASeq/man/IRanges-methods.Rd easyRNASeq/man/Rsamtools-methods.Rd easyRNASeq/man/ShortRead-methods.Rd easyRNASeq/man/basename-methods.Rd easyRNASeq/man/easyRNASeq-AnnotParam-accessors.Rd easyRNASeq/man/easyRNASeq-AnnotParam-class.Rd easyRNASeq/man/easyRNASeq-AnnotParam.Rd easyRNASeq/man/easyRNASeq-BamFileList.Rd easyRNASeq/man/easyRNASeq-BamParam-accessors.Rd easyRNASeq/man/easyRNASeq-BamParam-class.Rd easyRNASeq/man/easyRNASeq-BamParam.Rd easyRNASeq/man/easyRNASeq-RnaSeqParam-accessors.Rd easyRNASeq/man/easyRNASeq-RnaSeqParam-class.Rd easyRNASeq/man/easyRNASeq-RnaSeqParam.Rd easyRNASeq/man/easyRNASeq-accessors.Rd easyRNASeq/man/easyRNASeq-annotation-internal-methods.Rd easyRNASeq/man/easyRNASeq-annotation-methods.Rd easyRNASeq/man/easyRNASeq-class.Rd easyRNASeq/man/easyRNASeq-correction-methods.Rd easyRNASeq/man/easyRNASeq-coverage-methods.Rd easyRNASeq/man/easyRNASeq-datasets.Rd easyRNASeq/man/easyRNASeq-defunct-annotation-methods.Rd easyRNASeq/man/easyRNASeq-defunct.Rd easyRNASeq/man/easyRNASeq-deprecated.Rd easyRNASeq/man/easyRNASeq-easyRNASeq.Rd easyRNASeq/man/easyRNASeq-global-variables.Rd easyRNASeq/man/easyRNASeq-internal-AnnotParam-methods.Rd easyRNASeq/man/easyRNASeq-internal-methods.Rd easyRNASeq/man/easyRNASeq-island-methods.Rd easyRNASeq/man/easyRNASeq-package.Rd easyRNASeq/man/easyRNASeq-simpleRNASeq.Rd easyRNASeq/man/easyRNASeq-summarization-internal-methods.Rd easyRNASeq/man/easyRNASeq-summarization-methods.Rd easyRNASeq/man/easyRNASeq-synthetic-transcripts.Rd easyRNASeq/man/edgeR-methods.Rd easyRNASeq/man/file.exists-methods.Rd easyRNASeq/man/genomeIntervals-methods.Rd easyRNASeq/man/parallel-methods.Rd easyRNASeq/man/print-methods.Rd easyRNASeq/man/show-methods.Rd
easyRNASeq/tests
easyRNASeq/tests/runTests.R
easyRNASeq/vignettes
easyRNASeq/vignettes/Bibliography
easyRNASeq/vignettes/Bibliography/References.bib
easyRNASeq/vignettes/easyRNASeq.Rnw
easyRNASeq/vignettes/easyRNASeq.png
easyRNASeq/vignettes/simpleRNASeq.Rmd

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