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. |
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. |
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 |
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 |
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 |
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 |
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 |
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. |
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 |
knownOrganisms | The following function are defunct: • 'easyRNASeq' • 'fetchCoverage' • 'fetchAnnotation' • 'knownOrganisms' |
knownOrganisms-defunct | Defunct annotation function |
librarySize | Accessors for RNAseq class |
librarySize-method | Accessors for RNAseq class |
librarySize<- | Accessors for RNAseq class |
librarySize<--method | Accessors for RNAseq class |
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. |
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' |
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 |
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. |
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 |
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. |
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 |
unsafeAppend | Extension of the GenomicRanges package |
unsafeAppend-method | Extension of the GenomicRanges package |
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 |
yieldSize | Accessors for BamParam class |
yieldSize-method | Accessors for BamParam class |
yieldSize-method | Accessors for RnaSeqParam class |
.get_cache | Manages the data necessary for the examples using BiocFileCache |
.get_cache-method | Manages the data necessary for the examples using BiocFileCache |