Count summarization and normalization for RNA-Seq data


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Documentation for package ‘easyRNASeq’ version 2.34.0

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

easyRNASeq-package 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