# Analysis of alternative splicing using RNA-Seq

## Documentation for package ‘ASpli’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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