Analysis of alternative splicing using RNA-Seq


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Documentation for package ‘ASpli’ version 1.0.0

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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