# Count summarization and normalization for RNA-Seq data.

## Documentation for package ‘easyRNASeq’ version 1.8.8

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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
as | Extension for the genomeIntervals package
as-method | Extension for the genomeIntervals package

## -- 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 | Count methods for RNAseq object

## -- F --

featureCounts | Count methods for RNAseq object
featureCounts-method | Count methods for RNAseq object
fetchAnnotation | Fetch genic annotation from a gff/gtf file or using biomaRt
fetchAnnotation-method | Fetch genic annotation from a gff/gtf file or using biomaRt
fetchCoverage | Compute the coverage from a Short Read Alignment file
fetchCoverage-method | Compute the coverage from a Short Read Alignment file
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 | Identify expressed regions de-novo

## -- G --

geneCounts | Count methods for RNAseq object
geneCounts-method | Count methods for RNAseq object
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 | Accessors for RNAseq class
genomicAnnotation<- | Accessors for RNAseq class
genomicAnnotation<--method | Accessors for RNAseq class
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 | Count methods for RNAseq object

## -- 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 | Method to print a RNAseq object

## -- 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 | Display the content of a RNAseq object

## -- T --

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