easyRNASeq: Count summarization and normalization for RNA-Seq data
Version 2.12.0

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
Bioconductor views GeneExpression Genetics Preprocessing RNASeq
Date of publicationNone
MaintainerNicolas Delhomme <nicolas.delhomme@umu.se>
LicenseArtistic-2.0
Version2.12.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("easyRNASeq")

Getting started

Package overview
A walkthrough the easyRNASeq package functionalities

Popular man pages

DESeq-methods: Extension for the DESeq package
easyRNASeq-annotation-methods: Get genic annotation from a gff3/gtf file or using biomaRt
easyRNASeq-AnnotParam: AnnotParam constructor
easyRNASeq-BamFileList: Get a BamFileList from a list of filenames
easyRNASeq-simpleRNASeq: simpleRNASeq method
easyRNASeq-synthetic-transcripts: Methods to create synthetic transcripts
ShortRead-methods: Methods extending the ShortRead package functionalities
See all...

All man pages Function index File listing

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.

Functions

.bestExonSummarization Man page
.catn Man page
.checkArguments Man page
.convertToUCSC Man page
.doBasicCount Man page
.doCount Man page
.extendCountList Man page
.extractIRangesList Man page
.geneModelAnnotation Man page
.geneModelSummarization Man page
.getArguments Man page
.getBmRange Man page
.getGffRange Man page
.getGtfRange Man page
.getName Man page
.getWidth Man page
.list.files Man page
.list.files-deprecated Man page
.normalizationDispatcher Man page
.onAttach Man page
.readGffGtf Man page
.validate Man page
ANNOTATION.TYPE Man page
AnnotParam Man page
AnnotParam class Man page
AnnotParam internal methods Man page
AnnotParam,GRanges-method Man page
AnnotParam,RangedData-method Man page
AnnotParam,character-method Man page
AnnotParam,missing-method Man page
AnnotParam-accessors Man page
AnnotParam-class Man page
AnnotParamCharacter-class Man page
AnnotParamObject-class Man page
BamFileList Man page
BamFileList-class Man page
BamParam Man page
BamParam class Man page
BamParam,ANY-method Man page
BamParam-accessors Man page
BamParam-class Man page
DESeq additional methods Man page
Defunct functions Man page
Deprecated functions Man page
GTF.FIELDS Man page
IRanges Man page
IRanges additional methods Man page
RNAseq Man page
RNAseq class Man page
RNAseq-class Man page
RPKM Man page
RPKM,RNAseq,ANY,ANY,ANY-method Man page
RPKM,RNAseq-method Man page
RPKM,matrix,ANY,vector,vector-method Man page
RangedData Man page
RangedData-class Man page
RangedSummarizedExperiment-class Man page
RnaSeqParam Man page
RnaSeqParam class Man page
RnaSeqParam,ANY-method Man page
RnaSeqParam-accessors Man page
RnaSeqParam-class Man page
RobinsonDelhomme2014 Man page
SRFilterResult Man page
ShortRead additional methods Man page
accessors Man page
alignData Man page
annotParam Man page
annotParam,RnaSeqParam-method Man page
assay Man page
bamParam Man page
bamParam,RnaSeqParam-method Man page
barcodePlot Man page
barcodePlot,AlignedRead-method Man page
barcodePlot,DNAStringSet-method Man page
barcodePlot,ShortReadQ-method Man page
basename Man page
basename methods Man page
basename,BamFile-method Man page
basename,BamFileList-method Man page
chastityFilter Man page Source code
chastityFilter,SRFilter-method Man page
chrSize Man page
chrSize,RNAseq-method Man page
chrSize<- Man page
chrSize<-,RNAseq,integer-method Man page
chrSize<-,RNAseq,list-method Man page
chromosomeFilter Man page
colnames Man page
colnames,GRanges-method Man page
colnames,GRangesList-method Man page
compose Man page
countBy Man page
countBy,RnaSeqParam-method Man page
createSyntheticTranscripts Man page
createSyntheticTranscripts,AnnotParamCharacter-method Man page
createSyntheticTranscripts,character-method Man page
datasource Man page
datasource,AnnotParam-method Man page
datasource,RnaSeqParam-method Man page
demultiplex Man page
demultiplex,AlignedRead-method Man page
demultiplex,DNAStringSet-method Man page
demultiplex,ShortReadQ-method Man page
easyRNASeq Man page
easyRNASeq AnnotParam accessors Man page
easyRNASeq AnnotParam constructor Man page
easyRNASeq BamParam accessors Man page
easyRNASeq BamParam constructor Man page
easyRNASeq GenomicRanges package extension Man page
easyRNASeq RnaSeqParam accessors Man page
easyRNASeq RnaSeqParam constructor Man page
easyRNASeq accessors Man page
easyRNASeq annotation internal methods Man page
easyRNASeq annotation methods Man page
easyRNASeq correction methods Man page
easyRNASeq coverage methods Man page
easyRNASeq defunct annotation methods Man page
easyRNASeq internal methods Man page
easyRNASeq island methods Man page
easyRNASeq package Man page
easyRNASeq package-package Man page
easyRNASeq summarization internal methods Man page
easyRNASeq summarization methods Man page
easyRNASeq,RNAseq-method Man page
easyRNASeq,character-method Man page
easyRNASeq-datasets Man page
easyRNASeq-deprecated Man page
easyRNASeq-global-variables Man page
easyRNASeq-package Man page
edgeR additional methods Man page
exonCounts Man page
exonCounts,RNAseq-method Man page
featureCounts Man page
featureCounts,RNAseq-method Man page
fetchAnnotation Man page
fetchAnnotation-defunct Man page
fetchCoverage Man page
fetchCoverage,RNAseq-method Man page
fetchCoverage-deprecated Man page
file.exists Man page
file.exists methods Man page
file.exists,BamFile-method Man page
fileName Man page
fileName,RNAseq-method Man page
fileName<- Man page
fileName<-,RNAseq-method Man page
findIslands Man page
findIslands,RNAseq-method Man page
geneCounts Man page
geneCounts,RNAseq-method Man page
geneModel Man page
geneModel,RNAseq-method Man page
geneModel<- Man page
geneModel<-,RNAseq-method Man page
genomeIntervals additional methods Man page
genomicAnnotation Man page
genomicAnnotation,RNAseq-method Man page
genomicAnnotation<- Man page
genomicAnnotation<-,RNAseq-method Man page
getAnnotation Man page
getAnnotation,AnnotParam-method Man page
getBamFileList Man page
getBamFileList,character-method Man page
islandCounts Man page
islandCounts,RNAseq-method Man page
knownOrganisms Man page
knownOrganisms-defunct Man page
librarySize Man page
librarySize,RNAseq-method Man page
librarySize<- Man page
librarySize<-,RNAseq-method Man page
list.files Source code
locfit Man page
lp Man page
multivariateConditions Man page
multivariateConditions,CountDataSet-method Man page
nFilter Man page
naPositionFilter Man page Source code
naPositionFilter,SRFilter-method Man page
newCountDataSet Man page
organismName Man page
organismName,RNAseq-method Man page
organismName<- Man page
organismName<-,RNAseq-method Man page
paired Man page
paired,BamParam-method Man page
paired,RnaSeqParam-method Man page
parallel additional methods Man page
parallelize Man page
parallelize,BamFileList,function-method Man page
parallelize,GRangesList,function-method Man page
parallelize,list,function-method Man page
parallelize,vector,function-method Man page
plotDispLSD Man page
plotDispLSD,CountDataSet-method Man page
plotDispersionEstimates Man page
plotDispersionEstimates,CountDataSet-method Man page
plotDispersionEstimates,DGEList-method Man page
plotNormalizationFactors Man page
plotNormalizationFactors,DGEList,character,character-method Man page
precision Man page
precision,RnaSeqParam-method Man page
print Man page
print methods Man page
print,AnnotParam-method Man page
print,BamParam-method Man page
print,RNAseq-method Man page
print,RnaSeqParam-method Man page
ranges Man page
ranges,RNAseq-method Man page
readCounts Man page
readCounts,RNAseq-method Man page
readCounts<- Man page
readCounts<-,RNAseq-method Man page
readCoverage Man page
readCoverage,RNAseq-method Man page
readCoverage<- Man page
readCoverage<-,RNAseq-method Man page
readIslands Man page
readIslands,RNAseq-method Man page
readIslands<- Man page
readIslands<-,RNAseq-method Man page
readLength Man page
readLength,RNAseq-method Man page
readLength<- Man page
readLength<-,RNAseq-method Man page
reduce Man page
reduce,RNAseq-method Man page
seqnames,RNAseq-method Man page
show methods Man page
show,AnnotParam-method Man page
show,BamParam-method Man page
show,RNAseq-method Man page
show,RnaSeqParam-method Man page
simpleRNASeq Man page
simpleRNASeq,BamFileList,RnaSeqParam-method Man page
strand Man page
strand,RNAseq-method Man page
strand<- Man page
strand<-,RNAseq,ANY-method Man page
strand<-,RNAseq-method Man page
stranded Man page
stranded,BamParam-method Man page
stranded,RnaSeqParam-method Man page
transcriptCounts Man page
transcriptCounts,RNAseq-method Man page
type Man page
type,AnnotParam-method Man page
type,Genome_intervals-method Man page
unsafeAppend Man page
unsafeAppend,GAlignments,GAlignments-method Man page
validate Man page
validate,BamFile-method Man page
validate,BamFileList-method Man page
yieldSize Man page
yieldSize,BamParam-method Man page
yieldSize,RnaSeqParam-method Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/AllClasses.R
R/AllGenerics.R
R/DESeq-methods.R
R/GenomicRanges-methods.R
R/IRanges-methods.R
R/Rsamtools-methods.R
R/ShortRead-methods.R
R/basename-methods.R
R/easyRNASeq-AnnotParam-accessors.R
R/easyRNASeq-AnnotParam.R
R/easyRNASeq-BamFileList.R
R/easyRNASeq-BamParam-accessors.R
R/easyRNASeq-BamParam.R
R/easyRNASeq-RnaSeqParam-accessors.R
R/easyRNASeq-RnaSeqParam.R
R/easyRNASeq-accessors.R
R/easyRNASeq-annotation.R
R/easyRNASeq-counts.R
R/easyRNASeq-coverage-methods.R
R/easyRNASeq-internal-AnnotParam-methods.R
R/easyRNASeq-internal-annotation.R
R/easyRNASeq-internal-counts.R
R/easyRNASeq-internal-methods.R
R/easyRNASeq-internal-normalize.R
R/easyRNASeq-islands.R
R/easyRNASeq-methods.R
R/easyRNASeq-normalize.R
R/easyRNASeq-package.R
R/easyRNASeq-simpleRNASeq.R
R/easyRNASeq-synthetic-transcripts.R
R/edgeR-methods.R
R/file.exists-methods.R
R/genomeIntervals-methods.R
R/parallel-methods.R
R/print-methods.R
R/show-methods.R
build
build/vignette.rds
data
data/RobinsonDelhomme2014.txt.gz
inst
inst/CITATION
inst/doc
inst/doc/easyRNASeq.R
inst/doc/easyRNASeq.Rnw
inst/doc/easyRNASeq.pdf
inst/doc/simpleRNASeq.R
inst/doc/simpleRNASeq.Rmd
inst/doc/simpleRNASeq.html
inst/unitTests
inst/unitTests/test_accessors.R
inst/unitTests/test_annotations.R
inst/unitTests/test_classes.R
inst/unitTests/test_extensions.R
inst/unitTests/test_methods.R
inst/unitTests/test_print.R
inst/unitTests/test_ranges.R
inst/unitTests/test_variables.R
man
man/DESeq-methods.Rd
man/GenomicRanges-methods.Rd
man/IRanges-methods.Rd
man/Rsamtools-methods.Rd
man/ShortRead-methods.Rd
man/basename-methods.Rd
man/easyRNASeq-AnnotParam-accessors.Rd
man/easyRNASeq-AnnotParam-class.Rd
man/easyRNASeq-AnnotParam.Rd
man/easyRNASeq-BamFileList.Rd
man/easyRNASeq-BamParam-accessors.Rd
man/easyRNASeq-BamParam-class.Rd
man/easyRNASeq-BamParam.Rd
man/easyRNASeq-RnaSeqParam-accessors.Rd
man/easyRNASeq-RnaSeqParam-class.Rd
man/easyRNASeq-RnaSeqParam.Rd
man/easyRNASeq-accessors.Rd
man/easyRNASeq-annotation-internal-methods.Rd
man/easyRNASeq-annotation-methods.Rd
man/easyRNASeq-class.Rd
man/easyRNASeq-correction-methods.Rd
man/easyRNASeq-coverage-methods.Rd
man/easyRNASeq-datasets.Rd
man/easyRNASeq-defunct-annotation-methods.Rd
man/easyRNASeq-defunct.Rd
man/easyRNASeq-deprecated.Rd
man/easyRNASeq-easyRNASeq.Rd
man/easyRNASeq-global-variables.Rd
man/easyRNASeq-internal-AnnotParam-methods.Rd
man/easyRNASeq-internal-methods.Rd
man/easyRNASeq-island-methods.Rd
man/easyRNASeq-package.Rd
man/easyRNASeq-simpleRNASeq.Rd
man/easyRNASeq-summarization-internal-methods.Rd
man/easyRNASeq-summarization-methods.Rd
man/easyRNASeq-synthetic-transcripts.Rd
man/edgeR-methods.Rd
man/file.exists-methods.Rd
man/genomeIntervals-methods.Rd
man/parallel-methods.Rd
man/print-methods.Rd
man/show-methods.Rd
tests
tests/runTests.R
vignettes
vignettes/Bibliography
vignettes/Bibliography/References.bib
vignettes/easyRNASeq.Rnw
vignettes/easyRNASeq.png
vignettes/simpleRNASeq.Rmd
easyRNASeq documentation built on May 20, 2017, 10:36 p.m.

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