API for easyRNASeq
Count summarization and normalization for RNA-Seq data

Global 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
.get_cache	Man page
.get_cache,ANY-method	Man page
.list.files	Man page Source code
.list.files-defunct	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,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
BiocFileCache methods	Man page
DESeq additional methods	Man page
Defunct functions	Man page
GRanges	Man page
GRanges-class	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
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
SummarizedExperiment	Man page
TUTORIAL.DATA	Man page
VIGNETTE.DATA	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 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-defunct	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
fetchData	Man page
fetchData,character-method	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,character-method	Man page
getBamFileList,character,missing-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
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
strandProtocol	Man page
strandProtocol,BamParam-method	Man page
strandProtocol,RnaSeqParam-method	Man page
stranded	Man page
stranded,BamParam-method	Man page
stranded,RnaSeqParam-method	Man page
transcriptCounts	Man page
transcriptCounts,RNAseq-method	Man page
tutorialData	Man page
tutorialData,ANY-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
vignetteData	Man page
vignetteData,ANY-method	Man page
yieldSize	Man page
yieldSize,BamParam-method	Man page
yieldSize,RnaSeqParam-method	Man page