Count summarization and normalization for RNA-Seq data.


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Documentation for package ‘easyRNASeq’ version 2.0.8

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

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

-- 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
coerce-method Extension for the genomeIntervals package
colnames Extension of the GenomicRanges package
colnames-method Extension of the GenomicRanges package
compose Count summarization and normalization pipeline for Next Generation Sequencing data.
count count method
count-method count method
countBy Accessors for RnaSeqParam class
countBy-method Accessors for RnaSeqParam class

-- 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: • 'lotDispersionEstimates,DGEList-method'
demultiplex Methods extending the ShortRead package functionalities
demultiplex-method Methods extending the ShortRead package functionalities
Deprecated functions The following function have been deprecated: • 'easyRNASeq' • 'fetchCoverage' • 'fetchAnnotation' • 'knownOrganisms'
DESeq additional methods Extension for the DESeq package

-- E --

easyRNASeq The following function have been deprecated: • '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 deprecated annotation methods Fetch genic annotation from a gff/gtf file or using biomaRt
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-deprecated easyRNASeq method
easyRNASeq-method The following function have been deprecated: • '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 have been deprecated: • 'easyRNASeq' • 'fetchCoverage' • 'fetchAnnotation' • 'knownOrganisms'
fetchAnnotation-deprecated Fetch genic annotation from a gff/gtf file or using biomaRt
fetchAnnotation-method The following function have been deprecated: • 'easyRNASeq' • 'fetchCoverage' • 'fetchAnnotation' • 'knownOrganisms'
fetchCoverage The following function have been deprecated: • 'easyRNASeq' • 'fetchCoverage' • 'fetchAnnotation' • 'knownOrganisms'
fetchCoverage-deprecated Compute the coverage from a Short Read Alignment file
fetchCoverage-method The following function have been deprecated: • 'easyRNASeq' • 'fetchCoverage' • 'fetchAnnotation' • 'knownOrganisms'
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 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 have been deprecated: • 'easyRNASeq' • 'fetchCoverage' • 'fetchAnnotation' • 'knownOrganisms'
knownOrganisms-deprecated Fetch genic annotation from a gff/gtf file or using biomaRt
knownOrganisms-method The following function have been deprecated: • 'easyRNASeq' • 'fetchCoverage' • 'fetchAnnotation' • 'knownOrganisms'

-- L --

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

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

-- O --

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

-- 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
plotDispersionEstimates Extension for the DESeq package
plotDispersionEstimates-method Extension for the DESeq package
plotDispersionEstimates-method The following function are defunct: • 'lotDispersionEstimates,DGEList-method'
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
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 --

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

-- T --

transcriptCounts Count methods for RNAseq object
transcriptCounts-method Count methods for RNAseq object
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

-- Y --

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