Count summarization and normalization for RNA-Seq data

Documentation for package ‘easyRNASeq’ version 2.34.0

Help Pages

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

Count summarization and normalization pipeline for Next Generation Sequencing data.

-- 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"
assay	Count summarization and normalization pipeline for Next Generation Sequencing data.

-- B --

BamFileList	Count summarization and normalization pipeline for Next Generation Sequencing data.
BamFileList-class	Count summarization and normalization pipeline for Next Generation Sequencing data.
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
chromosomeFilter	Count summarization and normalization pipeline for Next Generation Sequencing data.
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
compose	Count summarization and normalization pipeline for Next Generation Sequencing data.
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 package	Count summarization and normalization pipeline for Next Generation Sequencing data.
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
GRanges	Count summarization and normalization pipeline for Next Generation Sequencing data.
GRanges-class	Count summarization and normalization pipeline for Next Generation Sequencing data.

-- I --

IRanges	Count summarization and normalization pipeline for Next Generation Sequencing data.
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
nFilter	Count summarization and normalization pipeline for Next Generation Sequencing data.

-- 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 --

RangedSummarizedExperiment-class	Count summarization and normalization pipeline for Next Generation Sequencing data.
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
SRFilterResult	Count summarization and normalization pipeline for Next Generation Sequencing data.
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
SummarizedExperiment	Count summarization and normalization pipeline for Next Generation Sequencing data.

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