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
.getWidth	easyRNASeq-internal-methods
.get_cache	BiocFileCache-methods
.get_cache,ANY-method	BiocFileCache-methods
.list.files	easyRNASeq-internal-methods
.list.files-defunct	easyRNASeq-internal-methods
.normalizationDispatcher	easyRNASeq-internal-methods
.onAttach	easyRNASeq-global-variables
.readGffGtf	easyRNASeq-annotation-internal-methods
.validate	easyRNASeq-internal-AnnotParam-methods
accessors	easyRNASeq-accessors
alignData	ShortRead-methods
ANNOTATION.TYPE	easyRNASeq-global-variables
AnnotParam	easyRNASeq-AnnotParam
annotParam	easyRNASeq-RnaSeqParam-accessors
AnnotParam class	easyRNASeq-AnnotParam-class
AnnotParam internal methods	easyRNASeq-internal-AnnotParam-methods
AnnotParam,character-method	easyRNASeq-AnnotParam
AnnotParam,GRanges-method	easyRNASeq-AnnotParam
AnnotParam,missing-method	easyRNASeq-AnnotParam
annotParam,RnaSeqParam-method	easyRNASeq-RnaSeqParam-accessors
AnnotParam-accessors	easyRNASeq-AnnotParam-accessors
AnnotParam-class	easyRNASeq-AnnotParam-class
AnnotParamCharacter-class	easyRNASeq-AnnotParam-class
AnnotParamObject-class	easyRNASeq-AnnotParam-class
assay	easyRNASeq-package
BamFileList	easyRNASeq-package
BamFileList-class	easyRNASeq-package
BamParam	easyRNASeq-BamParam
bamParam	easyRNASeq-RnaSeqParam-accessors
BamParam class	easyRNASeq-BamParam-class
BamParam,ANY-method	easyRNASeq-BamParam
bamParam,RnaSeqParam-method	easyRNASeq-RnaSeqParam-accessors
BamParam-accessors	easyRNASeq-BamParam-accessors
BamParam-class	easyRNASeq-BamParam-class
barcodePlot	ShortRead-methods
barcodePlot,AlignedRead-method	ShortRead-methods
barcodePlot,DNAStringSet-method	ShortRead-methods
barcodePlot,ShortReadQ-method	ShortRead-methods
basename	basename-methods
basename methods	basename-methods
basename,BamFile-method	basename-methods
basename,BamFileList-method	basename-methods
BiocFileCache methods	BiocFileCache-methods
chastityFilter	ShortRead-methods
chastityFilter,SRFilter-method	ShortRead-methods
chromosomeFilter	easyRNASeq-package
chrSize	easyRNASeq-accessors
chrSize,RNAseq-method	easyRNASeq-accessors
chrSize<-	easyRNASeq-accessors
chrSize<-,RNAseq,integer-method	easyRNASeq-accessors
chrSize<-,RNAseq,list-method	easyRNASeq-accessors
colnames	GenomicRanges-methods
colnames,GRanges-method	GenomicRanges-methods
colnames,GRangesList-method	GenomicRanges-methods
compose	easyRNASeq-package
countBy	easyRNASeq-RnaSeqParam-accessors
countBy,RnaSeqParam-method	easyRNASeq-RnaSeqParam-accessors
createSyntheticTranscripts	easyRNASeq-synthetic-transcripts
createSyntheticTranscripts,AnnotParamCharacter-method	easyRNASeq-synthetic-transcripts
createSyntheticTranscripts,character-method	easyRNASeq-synthetic-transcripts
datasource	easyRNASeq-AnnotParam-accessors
datasource,AnnotParam-method	easyRNASeq-AnnotParam-accessors
datasource,RnaSeqParam-method	easyRNASeq-RnaSeqParam-accessors
Defunct functions	easyRNASeq-defunct
demultiplex	ShortRead-methods
demultiplex,AlignedRead-method	ShortRead-methods
demultiplex,DNAStringSet-method	ShortRead-methods
demultiplex,ShortReadQ-method	ShortRead-methods
DESeq additional methods	DESeq-methods
easyRNASeq	easyRNASeq-defunct
easyRNASeq accessors	easyRNASeq-accessors
easyRNASeq annotation internal methods	easyRNASeq-annotation-internal-methods
easyRNASeq annotation methods	easyRNASeq-annotation-methods
easyRNASeq AnnotParam accessors	easyRNASeq-AnnotParam-accessors
easyRNASeq AnnotParam constructor	easyRNASeq-AnnotParam
easyRNASeq BamParam accessors	easyRNASeq-BamParam-accessors
easyRNASeq BamParam constructor	easyRNASeq-BamParam
easyRNASeq correction methods	easyRNASeq-correction-methods
easyRNASeq coverage methods	easyRNASeq-coverage-methods
easyRNASeq defunct annotation methods	easyRNASeq-defunct-annotation-methods
easyRNASeq GenomicRanges package extension	GenomicRanges-methods
easyRNASeq internal methods	easyRNASeq-internal-methods
easyRNASeq island methods	easyRNASeq-island-methods
easyRNASeq package	easyRNASeq-package
easyRNASeq RnaSeqParam accessors	easyRNASeq-RnaSeqParam-accessors
easyRNASeq RnaSeqParam constructor	easyRNASeq-RnaSeqParam
easyRNASeq summarization internal methods	easyRNASeq-summarization-internal-methods
easyRNASeq summarization methods	easyRNASeq-summarization-methods
easyRNASeq,character-method	easyRNASeq-easyRNASeq
easyRNASeq,RNAseq-method	easyRNASeq-defunct
easyRNASeq-datasets	easyRNASeq-datasets
easyRNASeq-defunct	easyRNASeq-easyRNASeq
easyRNASeq-global-variables	easyRNASeq-global-variables
edgeR additional methods	edgeR-methods
exonCounts	easyRNASeq-summarization-methods
exonCounts,RNAseq-method	easyRNASeq-summarization-methods
featureCounts	easyRNASeq-summarization-methods
featureCounts,RNAseq-method	easyRNASeq-summarization-methods
fetchAnnotation	easyRNASeq-defunct
fetchAnnotation-defunct	easyRNASeq-defunct-annotation-methods
fetchCoverage	easyRNASeq-defunct
fetchCoverage,RNAseq-method	easyRNASeq-defunct
fetchCoverage-deprecated	easyRNASeq-coverage-methods
fetchData	BiocFileCache-methods
fetchData,character-method	BiocFileCache-methods
file.exists	file.exists-methods
file.exists methods	file.exists-methods
file.exists,BamFile-method	file.exists-methods
fileName	easyRNASeq-accessors
fileName,RNAseq-method	easyRNASeq-accessors
fileName<-	easyRNASeq-accessors
fileName<-,RNAseq-method	easyRNASeq-accessors
findIslands	easyRNASeq-island-methods
findIslands,RNAseq-method	easyRNASeq-island-methods
geneCounts	easyRNASeq-summarization-methods
geneCounts,RNAseq-method	easyRNASeq-summarization-methods
geneModel	easyRNASeq-accessors
geneModel,RNAseq-method	easyRNASeq-accessors
geneModel<-	easyRNASeq-accessors
geneModel<-,RNAseq-method	easyRNASeq-accessors
genomeIntervals additional methods	genomeIntervals-methods
genomicAnnotation	easyRNASeq-accessors
genomicAnnotation,RNAseq-method	easyRNASeq-accessors
genomicAnnotation<-	easyRNASeq-accessors
genomicAnnotation<-,RNAseq-method	easyRNASeq-accessors
getAnnotation	easyRNASeq-annotation-methods
getAnnotation,AnnotParam-method	easyRNASeq-annotation-methods
getBamFileList	easyRNASeq-BamFileList
getBamFileList,character,character-method	easyRNASeq-BamFileList
getBamFileList,character,missing-method	easyRNASeq-BamFileList
GRanges	easyRNASeq-package
GRanges-class	easyRNASeq-package
GTF.FIELDS	easyRNASeq-global-variables
IRanges	easyRNASeq-package
IRanges additional methods	IRanges-methods
islandCounts	easyRNASeq-summarization-methods
islandCounts,RNAseq-method	easyRNASeq-summarization-methods
knownOrganisms	easyRNASeq-defunct
knownOrganisms-defunct	easyRNASeq-defunct-annotation-methods
librarySize	easyRNASeq-accessors
librarySize,RNAseq-method	easyRNASeq-accessors
librarySize<-	easyRNASeq-accessors
librarySize<-,RNAseq-method	easyRNASeq-accessors
locfit	DESeq-methods
lp	DESeq-methods
multivariateConditions	DESeq-methods
multivariateConditions,CountDataSet-method	DESeq-methods
naPositionFilter	ShortRead-methods
naPositionFilter,SRFilter-method	ShortRead-methods
newCountDataSet	DESeq-methods
nFilter	easyRNASeq-package
organismName	easyRNASeq-defunct
organismName,RNAseq-method	easyRNASeq-defunct
organismName<-	easyRNASeq-defunct
organismName<-,RNAseq-method	easyRNASeq-defunct
paired	easyRNASeq-BamParam-accessors
paired,BamParam-method	easyRNASeq-BamParam-accessors
paired,RnaSeqParam-method	easyRNASeq-RnaSeqParam-accessors
parallel additional methods	parallel-methods
parallelize	parallel-methods
parallelize,BamFileList,function-method	parallel-methods
parallelize,GRangesList,function-method	parallel-methods
parallelize,list,function-method	parallel-methods
parallelize,vector,function-method	parallel-methods
plotDispersionEstimates	DESeq-methods
plotDispersionEstimates,CountDataSet-method	DESeq-methods
plotDispersionEstimates,DGEList-method	easyRNASeq-defunct
plotDispLSD	DESeq-methods
plotDispLSD,CountDataSet-method	DESeq-methods
plotNormalizationFactors	edgeR-methods
plotNormalizationFactors,DGEList,character,character-method	edgeR-methods
precision	easyRNASeq-RnaSeqParam-accessors
precision,RnaSeqParam-method	easyRNASeq-RnaSeqParam-accessors
print	print-methods
print methods	print-methods
print,AnnotParam-method	print-methods
print,BamParam-method	print-methods
print,RNAseq-method	print-methods
print,RnaSeqParam-method	print-methods
RangedSummarizedExperiment-class	easyRNASeq-package
ranges	IRanges-methods
ranges,RNAseq-method	IRanges-methods
readCounts	easyRNASeq-accessors
readCounts,RNAseq-method	easyRNASeq-accessors
readCounts<-	easyRNASeq-accessors
readCounts<-,RNAseq-method	easyRNASeq-accessors
readCoverage	easyRNASeq-accessors
readCoverage,RNAseq-method	easyRNASeq-accessors
readCoverage<-	easyRNASeq-accessors
readCoverage<-,RNAseq-method	easyRNASeq-accessors
readIslands	easyRNASeq-accessors
readIslands,RNAseq-method	easyRNASeq-accessors
readIslands<-	easyRNASeq-accessors
readIslands<-,RNAseq-method	easyRNASeq-accessors
readLength	easyRNASeq-accessors
readLength,RNAseq-method	easyRNASeq-accessors
readLength<-	easyRNASeq-accessors
readLength<-,RNAseq-method	easyRNASeq-accessors
reduce	easyRNASeq-internal-methods
reduce,RNAseq-method	easyRNASeq-internal-methods
RNAseq	easyRNASeq-class
RNAseq class	easyRNASeq-class
RNAseq-class	easyRNASeq-class
RnaSeqParam	easyRNASeq-RnaSeqParam
RnaSeqParam class	easyRNASeq-RnaSeqParam-class
RnaSeqParam,ANY-method	easyRNASeq-RnaSeqParam
RnaSeqParam-accessors	easyRNASeq-RnaSeqParam-accessors
RnaSeqParam-class	easyRNASeq-RnaSeqParam-class
RobinsonDelhomme2014	easyRNASeq-datasets
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-correction-methods
seqnames,RNAseq-method	easyRNASeq-accessors
ShortRead additional methods	ShortRead-methods
show methods	show-methods
show,AnnotParam-method	show-methods
show,BamParam-method	show-methods
show,RNAseq-method	show-methods
show,RnaSeqParam-method	show-methods
simpleRNASeq	easyRNASeq-simpleRNASeq
simpleRNASeq,BamFileList,RnaSeqParam-method	easyRNASeq-simpleRNASeq
SRFilterResult	easyRNASeq-package
strand	easyRNASeq-internal-methods
strand,RNAseq-method	easyRNASeq-internal-methods
strand<-	easyRNASeq-internal-methods
strand<-,RNAseq,ANY-method	easyRNASeq-internal-methods
strand<-,RNAseq-method	easyRNASeq-internal-methods
stranded	easyRNASeq-BamParam-accessors
stranded,BamParam-method	easyRNASeq-BamParam-accessors
stranded,RnaSeqParam-method	easyRNASeq-RnaSeqParam-accessors
strandProtocol	easyRNASeq-BamParam-accessors
strandProtocol,BamParam-method	easyRNASeq-BamParam-accessors
strandProtocol,RnaSeqParam-method	easyRNASeq-RnaSeqParam-accessors
SummarizedExperiment	easyRNASeq-package
transcriptCounts	easyRNASeq-summarization-methods
transcriptCounts,RNAseq-method	easyRNASeq-summarization-methods
TUTORIAL.DATA	easyRNASeq-global-variables
tutorialData	BiocFileCache-methods
tutorialData,ANY-method	BiocFileCache-methods
type	easyRNASeq-package
type,AnnotParam-method	easyRNASeq-AnnotParam-accessors
type,Genome_intervals-method	genomeIntervals-methods
unsafeAppend	GenomicRanges-methods
unsafeAppend,GAlignments,GAlignments-method	GenomicRanges-methods
validate	Rsamtools-methods
validate,BamFile-method	Rsamtools-methods
validate,BamFileList-method	Rsamtools-methods
VIGNETTE.DATA	easyRNASeq-global-variables
vignetteData	BiocFileCache-methods
vignetteData,ANY-method	BiocFileCache-methods
yieldSize	easyRNASeq-BamParam-accessors
yieldSize,BamParam-method	easyRNASeq-BamParam-accessors
yieldSize,RnaSeqParam-method	easyRNASeq-RnaSeqParam-accessors
