# Count summarization and normalization for RNA-Seq data

## Documentation for package ‘easyRNASeq’ version 2.40.1

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

## Help Pages

A B C D E F G I K L N O P R S T U V Y misc

## -- A --

accessors | Accessors for RNAseq class
alignData | Methods extending the ShortRead package functionalities
AnnotParam | AnnotParam constructor
annotParam | Accessors for RnaSeqParam class
AnnotParam class | Class "AnnotParam"
AnnotParam-accessors | Accessors for AnnotParam class
AnnotParam-class | Class "AnnotParam"
AnnotParam-method | AnnotParam constructor
annotParam-method | Accessors for RnaSeqParam class
AnnotParamCharacter-class | Class "AnnotParam"
AnnotParamObject-class | Class "AnnotParam"

## -- B --

BamParam | BamParam constructor
bamParam | Accessors for RnaSeqParam class
BamParam class | Class "BamParam"
BamParam-accessors | Accessors for BamParam class
BamParam-class | Class "BamParam"
BamParam-method | BamParam constructor
bamParam-method | Accessors for RnaSeqParam class
barcodePlot | Methods extending the ShortRead package functionalities
barcodePlot-method | Methods extending the ShortRead package functionalities
basename | Extend the basename function to display Rsamtools BamFile class basename
basename methods | Extend the basename function to display Rsamtools BamFile class basename
basename-method | Extend the basename function to display Rsamtools BamFile class basename
BiocFileCache methods | Manages the data necessary for the examples using BiocFileCache

## -- 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
colnames | Extension of the GenomicRanges package
colnames-method | Extension of the GenomicRanges package
countBy | Accessors for RnaSeqParam class
countBy-method | Accessors for RnaSeqParam class
createSyntheticTranscripts | Methods to create synthetic transcripts
createSyntheticTranscripts-method | Methods to create synthetic transcripts

## -- D --

datasource | Accessors for AnnotParam class
datasource-method | Accessors for AnnotParam class
datasource-method | Accessors for RnaSeqParam class
Defunct functions | The following function are defunct: * 'easyRNASeq' * 'fetchCoverage' * 'fetchAnnotation' * 'knownOrganisms'
demultiplex | Methods extending the ShortRead package functionalities
demultiplex-method | Methods extending the ShortRead package functionalities

## -- E --

easyRNASeq | The following function are defunct: * 'easyRNASeq' * 'fetchCoverage' * 'fetchAnnotation' * 'knownOrganisms'
easyRNASeq accessors | Accessors for RNAseq class
easyRNASeq annotation methods | Get genic annotation from a gff3/gtf file or using biomaRt
easyRNASeq AnnotParam accessors | Accessors for AnnotParam class
easyRNASeq AnnotParam constructor | AnnotParam constructor
easyRNASeq BamParam accessors | Accessors for BamParam class
easyRNASeq BamParam constructor | BamParam constructor
easyRNASeq correction methods | easyRNASeq count table correction to RPKM
easyRNASeq coverage methods | Compute the coverage from a Short Read Alignment file
easyRNASeq defunct annotation methods | Defunct annotation function
easyRNASeq GenomicRanges package extension | Extension of the GenomicRanges package
easyRNASeq island methods | Identify expressed regions de-novo
easyRNASeq RnaSeqParam accessors | Accessors for RnaSeqParam class
easyRNASeq RnaSeqParam constructor | RnaSeqParam constructor
easyRNASeq summarization methods | Count methods for RNAseq object
easyRNASeq-datasets | Dataset included in the package
easyRNASeq-defunct | easyRNASeq method
easyRNASeq-method | The following function are defunct: * 'easyRNASeq' * 'fetchCoverage' * 'fetchAnnotation' * 'knownOrganisms'
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 | The following function are defunct: * 'easyRNASeq' * 'fetchCoverage' * 'fetchAnnotation' * 'knownOrganisms'
fetchAnnotation-defunct | Defunct annotation function
fetchCoverage | The following function are defunct: * 'easyRNASeq' * 'fetchCoverage' * 'fetchAnnotation' * 'knownOrganisms'
fetchCoverage-deprecated | Compute the coverage from a Short Read Alignment file
fetchCoverage-method | The following function are defunct: * 'easyRNASeq' * 'fetchCoverage' * 'fetchAnnotation' * 'knownOrganisms'
fetchData | Manages the data necessary for the examples using BiocFileCache
fetchData-method | Manages the data necessary for the examples using BiocFileCache
file.exists | Extend the file.exists function to check the path slot of a Rsamtools BamFile class for existence
file.exists methods | Extend the file.exists function to check the path slot of a Rsamtools BamFile class for existence
file.exists-method | Extend the file.exists function to check the path slot of a Rsamtools BamFile class for existence
fileName | Accessors for RNAseq class
fileName-method | Accessors for RNAseq class
fileName<- | Accessors for RNAseq class
fileName<--method | Accessors for RNAseq class
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 | Accessors for RNAseq class
geneModel<- | Accessors for RNAseq class
geneModel<--method | Accessors for RNAseq class
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
getAnnotation | Get genic annotation from a gff3/gtf file or using biomaRt
getAnnotation-method | Get genic annotation from a gff3/gtf file or using biomaRt
getBamFileList | Get a BamFileList from a list of filenames
getBamFileList-method | Get a BamFileList from a list of filenames

## -- I --

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

## -- K --

knownOrganisms | The following function are defunct: * 'easyRNASeq' * 'fetchCoverage' * 'fetchAnnotation' * 'knownOrganisms'
knownOrganisms-defunct | Defunct annotation function

## -- L --

librarySize | Accessors for RNAseq class
librarySize-method | Accessors for RNAseq class
librarySize<- | Accessors for RNAseq class
librarySize<--method | Accessors for RNAseq class

## -- N --

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

## -- O --

organismName | The following function are defunct: * 'easyRNASeq' * 'fetchCoverage' * 'fetchAnnotation' * 'knownOrganisms'
organismName-method | The following function are defunct: * 'easyRNASeq' * 'fetchCoverage' * 'fetchAnnotation' * 'knownOrganisms'
organismName<- | The following function are defunct: * 'easyRNASeq' * 'fetchCoverage' * 'fetchAnnotation' * 'knownOrganisms'
organismName<--method | The following function are defunct: * 'easyRNASeq' * 'fetchCoverage' * 'fetchAnnotation' * 'knownOrganisms'

## -- P --

paired | Accessors for BamParam class
paired-method | Accessors for BamParam class
paired-method | Accessors for RnaSeqParam class
parallel additional methods | parallel additional methods
parallelize | parallel additional methods
parallelize-method | parallel additional methods
plotNormalizationFactors | Extension for the edgeR package
plotNormalizationFactors-method | Extension for the edgeR package
precision | Accessors for RnaSeqParam class
precision-method | Accessors for RnaSeqParam class
print | Pretty print the content of classes from the easyRNASeq package.
print methods | Pretty print the content of classes from the easyRNASeq package.
print-method | Pretty print the content of classes from the easyRNASeq package.

## -- R --

ranges | Extension of the IRanges package
ranges-method | Extension of the IRanges package
readCounts | Accessors for RNAseq class
readCounts-method | Accessors for RNAseq class
readCounts<- | Accessors for RNAseq class
readCounts<--method | Accessors for RNAseq class
readCoverage | Accessors for RNAseq class
readCoverage-method | Accessors for RNAseq class
readCoverage<- | Accessors for RNAseq class
readCoverage<--method | Accessors for RNAseq class
readIslands | Accessors for RNAseq class
readIslands-method | Accessors for RNAseq class
readIslands<- | Accessors for RNAseq class
readIslands<--method | Accessors for RNAseq class
readLength | Accessors for RNAseq class
readLength-method | Accessors for RNAseq class
readLength<- | Accessors for RNAseq class
readLength<--method | Accessors for RNAseq class
RNAseq | Class "RNAseq"
RNAseq class | Class "RNAseq"
RNAseq-class | Class "RNAseq"
RnaSeqParam | RnaSeqParam constructor
RnaSeqParam class | Class "RnaSeqParam"
RnaSeqParam-accessors | Accessors for RnaSeqParam class
RnaSeqParam-class | Class "RnaSeqParam"
RnaSeqParam-method | RnaSeqParam constructor
RobinsonDelhomme2014 | Dataset included in the package
RPKM | easyRNASeq count table correction to RPKM
RPKM-method | easyRNASeq count table correction to RPKM

## -- S --

seqnames-method | Accessors for RNAseq class
ShortRead additional methods | Methods extending the ShortRead package functionalities
show methods | Display the content of classes from the easyRNASeq package.
show-method | Display the content of classes from the easyRNASeq package.
simpleRNASeq | simpleRNASeq method
simpleRNASeq-method | simpleRNASeq method
stranded | Accessors for BamParam class
stranded-method | Accessors for BamParam class
stranded-method | Accessors for RnaSeqParam class
strandProtocol | Accessors for BamParam class
strandProtocol-method | Accessors for BamParam class
strandProtocol-method | Accessors for RnaSeqParam class

## -- T --

transcriptCounts | Count methods for RNAseq object
transcriptCounts-method | Count methods for RNAseq object
tutorialData | Manages the data necessary for the examples using BiocFileCache
tutorialData-method | Manages the data necessary for the examples using BiocFileCache
type-method | Accessors for AnnotParam class
type-method | Extension for the genomeIntervals package

## -- U --

unsafeAppend | Extension of the GenomicRanges package
unsafeAppend-method | Extension of the GenomicRanges package

## -- V --

validate | Extension of the Rsamtools package
validate-method | Extension of the Rsamtools package
vignetteData | Manages the data necessary for the examples using BiocFileCache
vignetteData-method | Manages the data necessary for the examples using BiocFileCache

## -- Y --

yieldSize | Accessors for BamParam class
yieldSize-method | Accessors for BamParam class
yieldSize-method | Accessors for RnaSeqParam class

## -- misc --

.get_cache | Manages the data necessary for the examples using BiocFileCache
.get_cache-method | Manages the data necessary for the examples using BiocFileCache