easyRNASeq package-package	easyRNASeq-package
easyRNASeq-package	easyRNASeq-package
.bestExonSummarization	easyRNASeq-summarization-internal-methods
.catn	easyRNASeq-internal-methods
.checkArguments	easyRNASeq-internal-methods
.convertToUCSC	easyRNASeq-internal-methods
.doBasicCount	easyRNASeq-summarization-internal-methods
.doCount	easyRNASeq-summarization-internal-methods
.extendCountList	easyRNASeq-summarization-internal-methods
.extractIRangesList	easyRNASeq-internal-methods
.geneModelAnnotation	easyRNASeq-annotation-internal-methods
.geneModelSummarization	easyRNASeq-summarization-internal-methods
.getArguments	easyRNASeq-internal-methods
.getBmRange	easyRNASeq-annotation-internal-methods
.getGffRange	easyRNASeq-annotation-internal-methods
.getGtfRange	easyRNASeq-annotation-internal-methods
.getName	easyRNASeq-internal-methods
.list.files	easyRNASeq-internal-methods
.normalizationDispatcher	easyRNASeq-internal-methods
.readGffGtf	easyRNASeq-annotation-internal-methods
accessors	easyRNASeq-accessors
barcodePlot	ShortRead-methods
barcodePlot,AlignedRead-method	ShortRead-methods
barcodePlot,DNAStringSet-method	ShortRead-methods
barcodePlot,ShortReadQ-method	ShortRead-methods
chastityFilter	ShortRead-methods
chastityFilter,SRFilter-method	ShortRead-methods
chrSize	easyRNASeq-accessors
chrSize,RNAseq-method	easyRNASeq-accessors
chrSize<-	easyRNASeq-accessors
chrSize<-,RNAseq,integer-method	easyRNASeq-accessors
chrSize<-,RNAseq,list-method	easyRNASeq-accessors
coerce,Genome_intervals,GRangesList-method	genomeIntervals-methods
coerce,Genome_intervals,RangedData-method	genomeIntervals-methods
colnames	GenomicRanges-methods
colnames,GenomicRanges-method	GenomicRanges-methods
colnames,GRangesList-method	GenomicRanges-methods
count	easyRNASeq-count
count,character-method	easyRNASeq-count
demultiplex	ShortRead-methods
demultiplex,AlignedRead-method	ShortRead-methods
demultiplex,DNAStringSet-method	ShortRead-methods
demultiplex,ShortReadQ-method	ShortRead-methods
DESeq additional methods	DESeq-methods
DESeq and edgeR common methods	DESeq-edgeR-common-methods
easyRNASeq	easyRNASeq-easyRNASeq
easyRNASeq accessors	easyRNASeq-accessors
easyRNASeq annotation internal methods	easyRNASeq-annotation-internal-methods
easyRNASeq annotation methods	easyRNASeq-annotation-methods
easyRNASeq correction methods	easyRNASeq-correction-methods
easyRNASeq coverage methods	easyRNASeq-coverage-methods
easyRNASeq internal methods	easyRNASeq-internal-methods
easyRNASeq island methods	easyRNASeq-island-methods
easyRNASeq package	easyRNASeq-package
easyRNASeq summarization internal methods	easyRNASeq-summarization-internal-methods
easyRNASeq summarization methods	easyRNASeq-summarization-methods
easyRNASeq,character-method	easyRNASeq-easyRNASeq
easyRNASeq,RNAseq-method	easyRNASeq-class
edgeR additional methods	edgeR-methods
exonCounts	easyRNASeq-summarization-methods
exonCounts,RNAseq-method	easyRNASeq-class
featureCounts	easyRNASeq-summarization-methods
featureCounts,RNAseq-method	easyRNASeq-class
fetchAnnotation	easyRNASeq-annotation-methods
fetchAnnotation,RNAseq-method	easyRNASeq-class
fetchCoverage	easyRNASeq-coverage-methods
fetchCoverage,RNAseq-method	easyRNASeq-class
fileName	easyRNASeq-accessors
fileName,RNAseq-method	easyRNASeq-class
fileName<-	easyRNASeq-accessors
fileName<-,RNAseq-method	easyRNASeq-class
findIslands	easyRNASeq-island-methods
findIslands,RNAseq-method	easyRNASeq-class
geneCounts	easyRNASeq-summarization-methods
geneCounts,RNAseq-method	easyRNASeq-class
geneModel	easyRNASeq-accessors
geneModel,RNAseq-method	easyRNASeq-class
geneModel<-	easyRNASeq-accessors
geneModel<-,RNAseq-method	easyRNASeq-class
genomeIntervals additional methods	genomeIntervals-methods
genomicAnnotation	easyRNASeq-accessors
genomicAnnotation,RNAseq-method	easyRNASeq-class
genomicAnnotation<-	easyRNASeq-accessors
genomicAnnotation<-,RNAseq-method	easyRNASeq-class
GenomicRanges additional methods	GenomicRanges-methods
IRanges additional methods	IRanges-methods
islandCounts	easyRNASeq-summarization-methods
islandCounts,RNAseq-method	easyRNASeq-class
knownOrganisms	easyRNASeq-annotation-methods
knownOrganisms,missing-method	easyRNASeq-annotation-methods
librarySize	easyRNASeq-accessors
librarySize,RNAseq-method	easyRNASeq-class
librarySize<-	easyRNASeq-accessors
librarySize<-,RNAseq-method	easyRNASeq-class
multivariateConditions	DESeq-methods
multivariateConditions,CountDataSet-method	DESeq-methods
naPositionFilter	ShortRead-methods
naPositionFilter,SRFilter-method	ShortRead-methods
organismName	easyRNASeq-accessors
organismName,RNAseq-method	easyRNASeq-class
organismName<-	easyRNASeq-accessors
organismName<-,RNAseq-method	easyRNASeq-class
parallel additional methods	parallel-methods
parallelize	parallel-methods
parallelize,GRangesList,function-method	parallel-methods
parallelize,list,function-method	parallel-methods
parallelize,vector,function-method	parallel-methods
plotDispersionEstimates	DESeq-edgeR-common-methods
plotDispersionEstimates,CountDataSet-method	DESeq-edgeR-common-methods
plotDispersionEstimates,DGEList-method	DESeq-edgeR-common-methods
plotNormalizationFactors	edgeR-methods
plotNormalizationFactors,DGEList,character,character-method	edgeR-methods
print	print-methods
print methods	print-methods
print,RNAseq-method	easyRNASeq-class
ranges	IRanges-methods
ranges,RNAseq-method	IRanges-methods
readCounts	easyRNASeq-accessors
readCounts,RNAseq-method	easyRNASeq-class
readCounts<-	easyRNASeq-accessors
readCounts<-,RNAseq-method	easyRNASeq-class
readCoverage	easyRNASeq-accessors
readCoverage,RNAseq-method	easyRNASeq-class
readCoverage<-	easyRNASeq-accessors
readCoverage<-,RNAseq-method	easyRNASeq-class
readIslands	easyRNASeq-accessors
readIslands,RNAseq-method	easyRNASeq-class
readIslands<-	easyRNASeq-accessors
readIslands<-,RNAseq-method	easyRNASeq-class
readLength	easyRNASeq-accessors
readLength,RNAseq-method	easyRNASeq-class
readLength<-	easyRNASeq-accessors
readLength<-,RNAseq-method	easyRNASeq-class
reduce	easyRNASeq-internal-methods
reduce,RNAseq-method	easyRNASeq-internal-methods
RNAseq	easyRNASeq-class
RNAseq class	easyRNASeq-class
RNAseq-class	easyRNASeq-class
RPKM	easyRNASeq-correction-methods
RPKM,matrix,ANY,vector,vector-method	easyRNASeq-correction-methods
RPKM,RNAseq,ANY,ANY,ANY-method	easyRNASeq-correction-methods
RPKM,RNAseq-method	easyRNASeq-class
ShortRead additional methods	ShortRead-methods
show methods	show-methods
show,RNAseq-method	easyRNASeq-class
strand	easyRNASeq-internal-methods
strand,RNAseq-method	easyRNASeq-internal-methods
strand<-	easyRNASeq-internal-methods
strand<-,RNAseq-method	easyRNASeq-internal-methods
transcriptCounts	easyRNASeq-summarization-methods
transcriptCounts,RNAseq-method	easyRNASeq-class
type,Genome_intervals-method	genomeIntervals-methods
