Count summarization and normalization for RNA-Seq data.

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Documentation for package ‘easyRNASeq’ version 1.2.5

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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
print 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"