easyRNASeq-package | Count summarization and normalization pipeline for Next Generation Sequencing data. |
accessors | Accessors for RNAseq class |
barcodePlot | Methods extending the ShortRead package functionalities |
barcodePlot-method | Methods extending the ShortRead package functionalities |
chastityFilter | Methods extending the ShortRead package functionalities |
chastityFilter-method | Methods extending the ShortRead package functionalities |
chrSize | Accessors for RNAseq class |
chrSize-method | Class "RNAseq" |
chrSize<- | Accessors for RNAseq class |
chrSize<--method | Class "RNAseq" |
coerce-method | Extension for the genomeIntervals package |
colnames | Extension of the GenomicRanges package |
colnames-method | Extension of the GenomicRanges package |
demultiplex | Methods extending the ShortRead package functionalities |
demultiplex-method | Methods extending the ShortRead package functionalities |
easyRNASeq | easyRNASeq method |
easyRNASeq-method | Class "RNAseq" |
easyRNASeq-method | easyRNASeq method |
exonCounts | Count methods for RNAseq object |
exonCounts-method | Class "RNAseq" |
featureCounts | Count methods for RNAseq object |
featureCounts-method | Class "RNAseq" |
fetchAnnotation | Fetch genic annotation from a gff/gtf file or using biomaRt |
fetchAnnotation-method | Class "RNAseq" |
fetchCoverage | Compute the coverage from a Short Read Alignment file |
fetchCoverage-method | Class "RNAseq" |
fileName | Accessors for RNAseq class |
fileName-method | Class "RNAseq" |
fileName<- | Accessors for RNAseq class |
fileName<--method | Class "RNAseq" |
findIslands | Identify expressed regions de-novo |
findIslands-method | Class "RNAseq" |
geneCounts | Count methods for RNAseq object |
geneCounts-method | Class "RNAseq" |
geneModel | Accessors for RNAseq class |
geneModel-method | Class "RNAseq" |
geneModel<- | Accessors for RNAseq class |
geneModel<--method | Class "RNAseq" |
genomicAnnotation | Accessors for RNAseq class |
genomicAnnotation-method | Class "RNAseq" |
genomicAnnotation<- | Accessors for RNAseq class |
genomicAnnotation<--method | Class "RNAseq" |
islandCounts | Count methods for RNAseq object |
islandCounts-method | Class "RNAseq" |
librarySize | Accessors for RNAseq class |
librarySize-method | Class "RNAseq" |
librarySize<- | Accessors for RNAseq class |
librarySize<--method | Class "RNAseq" |
multivariateConditions | Extension for the DESeq package |
multivariateConditions-method | Extension for the DESeq package |
naPositionFilter | Methods extending the ShortRead package functionalities |
naPositionFilter-method | Methods extending the ShortRead package functionalities |
organismName | Accessors for RNAseq class |
organismName-method | Class "RNAseq" |
organismName<- | Accessors for RNAseq class |
organismName<--method | Class "RNAseq" |
plotDispersionEstimates | DESeq and edgeR common methods |
plotDispersionEstimates-method | DESeq and edgeR common methods |
plotNormalizationFactors | Extension for the edgeR package |
plotNormalizationFactors-method | Extension for the edgeR package |
Method to print a RNAseq object | |
print-method | Class "RNAseq" |
ranges | Extension of the IRanges package |
ranges-method | Extension of the IRanges package |
readCounts | Accessors for RNAseq class |
readCounts-method | Class "RNAseq" |
readCounts<- | Accessors for RNAseq class |
readCounts<--method | Class "RNAseq" |
readCoverage | Accessors for RNAseq class |
readCoverage-method | Class "RNAseq" |
readCoverage<- | Accessors for RNAseq class |
readCoverage<--method | Class "RNAseq" |
readIslands | Accessors for RNAseq class |
readIslands-method | Class "RNAseq" |
readIslands<- | Accessors for RNAseq class |
readIslands<--method | Class "RNAseq" |
readLength | Accessors for RNAseq class |
readLength-method | Class "RNAseq" |
readLength<- | Accessors for RNAseq class |
readLength<--method | Class "RNAseq" |
RNAseq | Class "RNAseq" |
RNAseq-class | Class "RNAseq" |
RPKM | easyRNASeq count table correction to RPKM |
RPKM-method | Class "RNAseq" |
RPKM-method | easyRNASeq count table correction to RPKM |
show-method | Class "RNAseq" |
show-methods | Display the content of a RNAseq object |
transcriptCounts | Count methods for RNAseq object |
transcriptCounts-method | Class "RNAseq" |