ASpli-package | Analysis of alternative splicing using RNAseq |
altPSI | Accessors for ASpliAS object |
altPSI-method | Class '"ASpliAS"' |
AsDiscover | Report PSI and PIR using experimental junctions |
AsDiscover-method | Class '"ASpliCounts"' |
ASpli | Analysis of alternative splicing using RNAseq |
ASpliAS-class | Class '"ASpliAS"' |
ASpliCounts | Class '"ASpliCounts"' |
ASpliCounts-class | Class '"ASpliCounts"' |
ASpliDU-class | Class '"ASpliDU"' |
ASpliFeatures-class | Class '"ASpliFeatures"' |
binGenome | Feature coordinates extraction |
binGenome-method | Feature coordinates extraction |
binGenome-methods | Feature coordinates extraction |
binsDU | Accessors for ASpliDU object |
binsDU-method | Class '"ASpliDU"' |
countsb | Accessors for ASpliCounts object |
countsb-method | Class '"ASpliCounts"' |
countse1i | Accessors for ASpliCounts object |
countse1i-method | Class '"ASpliCounts"' |
countsg | Accessors for ASpliCounts object |
countsg-method | Class '"ASpliCounts"' |
countsie2 | Accessors for ASpliCounts object |
countsie2-method | Class '"ASpliCounts"' |
countsj | Accessors for ASpliCounts object |
countsj-method | Class '"ASpliCounts"' |
DUreport | Differential gene expression and differential bin/junction usage estimation |
DUreport-method | Class '"ASpliCounts"' |
DUreport_DEXSeq | Differential gene expression and differential bin/junction usage estimation |
DUreport_DEXSeq-method | Class '"ASpliCounts"' |
esPSI | Accessors for ASpliAS object |
esPSI-method | Class '"ASpliAS"' |
featuresb | Accessors for ASpliFeatures object |
featuresb-method | Class '"ASpliFeatures"' |
featuresg | Accessors for ASpliFeatures object |
featuresg-method | Class '"ASpliFeatures"' |
featuresj | Accessors for ASpliFeatures object |
featuresj-method | Class '"ASpliFeatures"' |
genesDE | Accessors for ASpliDU object |
genesDE-method | Class '"ASpliDU"' |
irPIR | Accessors for ASpliAS object |
irPIR-method | Class '"ASpliAS"' |
joint | Accessors for ASpliAS object |
joint-method | Class '"ASpliAS"' |
junctionsDU | Accessors for ASpliDU object |
junctionsDU-method | Class '"ASpliDU"' |
junctionsPIR | Accessors for ASpliAS object |
junctionsPIR-method | Class '"ASpliAS"' |
junctionsPSI | Accessors for ASpliAS object |
junctionsPSI-method | Class '"ASpliAS"' |
loadBAM | Load BAM files |
plotTopTags | Coverage plots |
rds | Divides read counts by gene and bin length |
rds-method | Class '"ASpliCounts"' |
rdsb | Accessors for ASpliCounts object |
rdsb-method | Class '"ASpliCounts"' |
rdsg | Accessors for ASpliCounts object |
rdsg-method | Class '"ASpliCounts"' |
readCounts | Summarize read overlaps |
readCounts-method | Class '"ASpliFeatures"' |
show-method | Display a summary of data contained in ASpliObjects |
show-methods | Display a summary of data contained in ASpliObjects |
writeAll | Write results |
writeAll-method | Write results |
writeAS | Write results |
writeAS-method | Class '"ASpliAS"' |
writeAS-methods | Write results |
writeCounts | Write results |
writeCounts-method | Class '"ASpliCounts"' |
writeCounts-methods | Write results |
writeDU | Write results |
writeDU-method | Class '"ASpliDU"' |
writeDU-methods | Write results |
writeRds | Write results |
writeRds-method | Class '"ASpliCounts"' |
writeRds-methods | Write results |