easyRNASeq: Count summarization and normalization for RNA-Seq data

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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.

Author
Nicolas Delhomme, Ismael Padioleau, Bastian Schiffthaler, Niklas Maehler
Date of publication
None
Maintainer
Nicolas Delhomme <nicolas.delhomme@umu.se>
License
Artistic-2.0
Version
2.10.0

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