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.

Functions

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

Files

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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