Count summarization and normalization for RNA-Seq data.

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Documentation for package ‘easyRNASeq’ version 1.6.4

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A B C D E F G I K L M N O P R S T

easyRNASeq package-package Count summarization and normalization pipeline for Next Generation Sequencing data.
easyRNASeq-package Count summarization and normalization pipeline for Next Generation Sequencing data.

-- A --

accessors Accessors for RNAseq class

-- B --

barcodePlot Methods extending the ShortRead package functionalities
barcodePlot-method Methods extending the ShortRead package functionalities

-- C --

chastityFilter Methods extending the ShortRead package functionalities
chastityFilter-method Methods extending the ShortRead package functionalities
chrSize Accessors for RNAseq class
chrSize-method Accessors for RNAseq class
chrSize<- Accessors for RNAseq class
chrSize<--method Accessors for RNAseq class
coerce-method Extension for the genomeIntervals package
colnames Extension of the GenomicRanges package
colnames-method Extension of the GenomicRanges package
count count method
count-method count method

-- D --

demultiplex Methods extending the ShortRead package functionalities
demultiplex-method Methods extending the ShortRead package functionalities
DESeq additional methods Extension for the DESeq package
DESeq and edgeR common methods DESeq and edgeR common methods

-- E --

easyRNASeq easyRNASeq method
easyRNASeq accessors Accessors for RNAseq class
easyRNASeq annotation methods Fetch genic annotation from a gff/gtf file or using biomaRt
easyRNASeq correction methods easyRNASeq count table correction to RPKM
easyRNASeq coverage methods Compute the coverage from a Short Read Alignment file
easyRNASeq island methods Identify expressed regions de-novo
easyRNASeq package Count summarization and normalization pipeline for Next Generation Sequencing data.
easyRNASeq summarization methods Count methods for RNAseq object
easyRNASeq-method Class "RNAseq"
easyRNASeq-method easyRNASeq method
edgeR additional methods Extension for the edgeR package
exonCounts Count methods for RNAseq object
exonCounts-method Class "RNAseq"

-- F --

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"

-- G --

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"
genomeIntervals additional methods Extension for the genomeIntervals package
genomicAnnotation Accessors for RNAseq class
genomicAnnotation-method Class "RNAseq"
genomicAnnotation<- Accessors for RNAseq class
genomicAnnotation<--method Class "RNAseq"
GenomicRanges additional methods Extension of the GenomicRanges package

-- I --

IRanges additional methods Extension of the IRanges package
islandCounts Count methods for RNAseq object
islandCounts-method Class "RNAseq"

-- K --

knownOrganisms Fetch genic annotation from a gff/gtf file or using biomaRt
knownOrganisms-method Fetch genic annotation from a gff/gtf file or using biomaRt

-- L --

librarySize Accessors for RNAseq class
librarySize-method Class "RNAseq"
librarySize<- Accessors for RNAseq class
librarySize<--method Class "RNAseq"

-- M --

multivariateConditions Extension for the DESeq package
multivariateConditions-method Extension for the DESeq package

-- N --

naPositionFilter Methods extending the ShortRead package functionalities
naPositionFilter-method Methods extending the ShortRead package functionalities

-- O --

organismName Accessors for RNAseq class
organismName-method Class "RNAseq"
organismName<- Accessors for RNAseq class
organismName<--method Class "RNAseq"

-- P --

parallel additional methods parallel additional methods
parallelize parallel additional methods
parallelize-method parallel additional methods
plotDispersionEstimates DESeq and edgeR common methods
plotDispersionEstimates-method DESeq and edgeR common methods
plotDispLSD Extension for the DESeq package
plotDispLSD-method Extension for the DESeq package
plotNormalizationFactors Extension for the edgeR package
plotNormalizationFactors-method Extension for the edgeR package
print Method to print a RNAseq object
print methods Method to print a RNAseq object
print-method Class "RNAseq"

-- R --

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"
RNAseq-class Class "RNAseq"
RPKM easyRNASeq count table correction to RPKM
RPKM-method Class "RNAseq"
RPKM-method easyRNASeq count table correction to RPKM

-- S --

ShortRead additional methods Methods extending the ShortRead package functionalities
show methods Display the content of a RNAseq object
show-method Class "RNAseq"

-- T --

transcriptCounts Count methods for RNAseq object
transcriptCounts-method Class "RNAseq"
type-method Extension for the genomeIntervals package