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. |
| 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 |
| 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' • 'plotDispersionEstimates,DGEList-method' |
| demultiplex | Methods extending the ShortRead package functionalities |
| demultiplex-method | Methods extending the ShortRead package functionalities |
| DESeq additional methods | Extension for the DESeq package |
| easyRNASeq | The following function are defunct: • 'easyRNASeq' • 'fetchCoverage' • 'fetchAnnotation' • 'knownOrganisms' • 'plotDispersionEstimates,DGEList-method' |
| 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' • 'plotDispersionEstimates,DGEList-method' |
| 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' • 'plotDispersionEstimates,DGEList-method' |
| fetchAnnotation-defunct | Defunct annotation function |
| fetchCoverage | The following function are defunct: • 'easyRNASeq' • 'fetchCoverage' • 'fetchAnnotation' • 'knownOrganisms' • 'plotDispersionEstimates,DGEList-method' |
| fetchCoverage-deprecated | Compute the coverage from a Short Read Alignment file |
| fetchCoverage-method | The following function are defunct: • 'easyRNASeq' • 'fetchCoverage' • 'fetchAnnotation' • 'knownOrganisms' • 'plotDispersionEstimates,DGEList-method' |
| 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 |
| 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' • 'plotDispersionEstimates,DGEList-method' |
| 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 |
| locfit | Extension for the DESeq package |
| lp | Extension for the DESeq package |
| multivariateConditions | Extension for the DESeq package |
| multivariateConditions-method | Extension for the DESeq package |
| naPositionFilter | Methods extending the ShortRead package functionalities |
| naPositionFilter-method | Methods extending the ShortRead package functionalities |
| newCountDataSet | Extension for the DESeq package |
| nFilter | Count summarization and normalization pipeline for Next Generation Sequencing data. |
| organismName | The following function are defunct: • 'easyRNASeq' • 'fetchCoverage' • 'fetchAnnotation' • 'knownOrganisms' • 'plotDispersionEstimates,DGEList-method' |
| organismName-method | The following function are defunct: • 'easyRNASeq' • 'fetchCoverage' • 'fetchAnnotation' • 'knownOrganisms' • 'plotDispersionEstimates,DGEList-method' |
| organismName<- | The following function are defunct: • 'easyRNASeq' • 'fetchCoverage' • 'fetchAnnotation' • 'knownOrganisms' • 'plotDispersionEstimates,DGEList-method' |
| organismName<--method | The following function are defunct: • 'easyRNASeq' • 'fetchCoverage' • 'fetchAnnotation' • 'knownOrganisms' • 'plotDispersionEstimates,DGEList-method' |
| 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: • 'easyRNASeq' • 'fetchCoverage' • 'fetchAnnotation' • 'knownOrganisms' • 'plotDispersionEstimates,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 |
| 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. |
| RangedData | Count summarization and normalization pipeline for Next Generation Sequencing data. |
| RangedData-class | Count summarization and normalization pipeline for Next Generation Sequencing data. |
| 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 |
| 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 |
| 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 |
| yieldSize | Accessors for BamParam class |
| yieldSize-method | Accessors for BamParam class |
| yieldSize-method | Accessors for RnaSeqParam class |