A B C D E F G I K L M N O P R S T
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 |
as | Extension for the genomeIntervals package |
as-method | Extension for the genomeIntervals package |
barcodePlot | Methods extending the ShortRead package functionalities |
barcodePlot-method | Methods extending the ShortRead package functionalities |
chastityFilter | Methods extending the ShortRead package functionalities |
chastityFilter-method | Methods extending the ShortRead package functionalities |
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 |
count | count method |
count-method | count method |
demultiplex | Methods extending the ShortRead package functionalities |
demultiplex-method | Methods extending the ShortRead package functionalities |
DESeq additional methods | Extension for the DESeq package |
DESeq and edgeR common methods | DESeq and edgeR common methods |
easyRNASeq | easyRNASeq method |
easyRNASeq accessors | Accessors for RNAseq class |
easyRNASeq annotation methods | Fetch genic annotation from a gff/gtf file or using biomaRt |
easyRNASeq correction methods | easyRNASeq count table correction to RPKM |
easyRNASeq coverage methods | Compute the coverage from a Short Read Alignment file |
easyRNASeq island methods | Identify expressed regions de-novo |
easyRNASeq package | Count summarization and normalization pipeline for Next Generation Sequencing data. |
easyRNASeq summarization methods | Count methods for RNAseq object |
easyRNASeq-method | Class "RNAseq" |
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 | Fetch genic annotation from a gff/gtf file or using biomaRt |
fetchAnnotation-method | Fetch genic annotation from a gff/gtf file or using biomaRt |
fetchCoverage | Compute the coverage from a Short Read Alignment file |
fetchCoverage-method | Compute the coverage from a Short Read Alignment file |
fileName | Accessors for RNAseq class |
fileName-method | Class "RNAseq" |
fileName<- | Accessors for RNAseq class |
fileName<--method | Class "RNAseq" |
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 | Class "RNAseq" |
geneModel<- | Accessors for RNAseq class |
geneModel<--method | Class "RNAseq" |
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 |
GenomicRanges additional methods | Extension of the GenomicRanges package |
IRanges additional methods | Extension of the IRanges package |
islandCounts | Count methods for RNAseq object |
islandCounts-method | Count methods for RNAseq object |
knownOrganisms | Fetch genic annotation from a gff/gtf file or using biomaRt |
knownOrganisms-method | Fetch genic annotation from a gff/gtf file or using biomaRt |
librarySize | Accessors for RNAseq class |
librarySize-method | Class "RNAseq" |
librarySize<- | Accessors for RNAseq class |
librarySize<--method | Class "RNAseq" |
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 |
organismName | Accessors for RNAseq class |
organismName-method | Class "RNAseq" |
organismName<- | Accessors for RNAseq class |
organismName<--method | Class "RNAseq" |
parallel additional methods | parallel additional methods |
parallelize | parallel additional methods |
parallelize-method | parallel additional methods |
plotDispersionEstimates | DESeq and edgeR common methods |
plotDispersionEstimates-method | DESeq and edgeR common methods |
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 |
Method to print a RNAseq object | |
print methods | Method to print a RNAseq object |
print-method | Method to print a RNAseq object |
ranges | Extension of the IRanges package |
ranges-method | Extension of the IRanges package |
readCounts | Accessors for RNAseq class |
readCounts-method | Class "RNAseq" |
readCounts<- | Accessors for RNAseq class |
readCounts<--method | Class "RNAseq" |
readCoverage | Accessors for RNAseq class |
readCoverage-method | Class "RNAseq" |
readCoverage<- | Accessors for RNAseq class |
readCoverage<--method | Class "RNAseq" |
readIslands | Accessors for RNAseq class |
readIslands-method | Class "RNAseq" |
readIslands<- | Accessors for RNAseq class |
readIslands<--method | Class "RNAseq" |
readLength | Accessors for RNAseq class |
readLength-method | Class "RNAseq" |
readLength<- | Accessors for RNAseq class |
readLength<--method | Class "RNAseq" |
RNAseq | Class "RNAseq" |
RNAseq class | Class "RNAseq" |
RNAseq-class | Class "RNAseq" |
RPKM | easyRNASeq count table correction to RPKM |
RPKM-method | Class "RNAseq" |
RPKM-method | easyRNASeq count table correction to RPKM |
ShortRead additional methods | Methods extending the ShortRead package functionalities |
show methods | Display the content of a RNAseq object |
show-method | Display the content of a RNAseq object |
transcriptCounts | Count methods for RNAseq object |
transcriptCounts-method | Count methods for RNAseq object |
type | Extension for the genomeIntervals package |
type-method | Extension for the genomeIntervals package |