ASpli: Analysis of alternative splicing using RNA-Seq
Version 1.2.1

Integrative pipeline for the analysis of alternative splicing using RNA-seq.

Browse man pages Browse package API and functions Browse package files

AuthorEstefania Mancini, Marcelo Yanovsky and Ariel Chernomoretz
Bioconductor views Alignment AlternativeSplicing Coverage DifferentialExpression DifferentialSplicing GeneExpression GenomeAnnotation RNASeq Sequencing TimeCourse Transcription
Date of publicationNone
MaintainerEstefania Mancini <emancini@leloir.org.ar>
LicenseGPL
Version1.2.1
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("ASpli")

Man pages

acc_AS: Accessors for ASpliAS object
acc_counts: Accessors for ASpliCounts object
acc_DU: Accessors for ASpliDU object
acc_features: Accessors for ASpliFeatures object
AsDiscover-methods: Report PSI and PIR using experimental junctions
ASpliAS-class: Class '"ASpliAS"'
ASpliCounts: Class '"ASpliCounts"'
ASpliCounts-class: Class '"ASpliCounts"'
ASpliDU-class: Class '"ASpliDU"'
ASpliFeatures-class: Class '"ASpliFeatures"'
ASpli-package: Analysis of alternative splicing using RNAseq
binGenome: Feature coordinates extraction
binGenome-methods: Feature coordinates extraction
DUreport: Differential gene expression and differential bin/junction...
DUreport_DEXSeq: Differential gene expression and differential bin/junction...
loadBAM: Load BAM files
plotTopTags: Coverage plots
rds: Divides read counts by gene and bin length
readCounts: Summarize read overlaps
show-methods: Display a summary of data contained in ASpliObjects
write: Write results
write-methods: Write results

Functions

ASpli Man page
ASpli-package Man page
ASpliAS-class Man page
ASpliCounts Man page
ASpliCounts-class Man page
ASpliDU-class Man page
ASpliFeatures-class Man page
AsDiscover Man page
AsDiscover,ASpliCounts-method Man page
DUreport Man page
DUreport,ASpliCounts-method Man page
DUreport_DEXSeq Man page
DUreport_DEXSeq,ASpliCounts-method Man page
altPSI Man page
altPSI,ASpliAS-method Man page
binGenome Man page
binGenome,TxDb-method Man page
binGenome-methods Man page
binsDU Man page Source code
binsDU,ASpliDU-method Man page
binsDU_DEXSeq Source code
counterBin Source code
counterGenes Source code
counterJbin Source code
counterJunctions Source code
countsb Man page
countsb,ASpliCounts-method Man page
countse1i Man page
countse1i,ASpliCounts-method Man page
countsg Man page
countsg,ASpliCounts-method Man page
countsie2 Man page
countsie2,ASpliCounts-method Man page
countsj Man page
countsj,ASpliCounts-method Man page
createGRangesExons Source code
createGRangesExpJunctions Source code
createGRangesGenes Source code
createGRangesIntrons Source code
createGRangesJunctions Source code
createGRangesTranscripts Source code
e2JPIR Source code
endJPSI Source code
esPSI Man page
esPSI,ASpliAS-method Man page
featuresb Man page
featuresb,ASpliFeatures-method Man page
featuresg Man page
featuresg,ASpliFeatures-method Man page
featuresj Man page
featuresj,ASpliFeatures-method Man page
filterByRdBinRATIO Source code
filterByRdGen Source code
filterByReads Source code
filterJunctionBySample Source code
findASBin Source code
genesDE Man page Source code
genesDE,ASpliDU-method Man page
genesDE_DESeq Source code
irPIR Man page
irPIR,ASpliAS-method Man page
joint Man page
joint,ASpliAS-method Man page
junctionsDU Man page
junctionsDU,ASpliDU-method Man page
junctionsDU_SUM Source code
junctionsDU_SUM_DEXSeq Source code
junctionsDiscover Source code
junctionsPIR Man page
junctionsPIR,ASpliAS-method Man page
junctionsPSI Man page
junctionsPSI,ASpliAS-method Man page
junctionsPSI_SUM Source code
loadBAM Man page Source code
normalizeByGenFeature Source code
ovBinJunction Source code
plotTopTags Man page Source code
rds Man page
rds,ASpliCounts-method Man page
rdsb Man page
rdsb,ASpliCounts-method Man page
rdsg Man page
rdsg,ASpliCounts-method Man page
readCounts Man page
readCounts,ASpliFeatures-method Man page
show,ASpliAS-method Man page
show,ASpliCounts-method Man page
show,ASpliDU-method Man page
show,ASpliFeatures-method Man page
show-methods Man page
startJPSI Source code
withinJPSI Source code
writeAS Man page
writeAS,ASpliAS-method Man page
writeAS-methods Man page
writeAll Man page
writeAll,ANY-method Man page
writeCounts Man page
writeCounts,ASpliCounts-method Man page
writeCounts-methods Man page
writeDU Man page
writeDU,ASpliDU-method Man page
writeDU-methods Man page
writeRds Man page
writeRds,ASpliCounts-method Man page
writeRds-methods Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/ASDiscover_functions.R
R/ASpli_methods.R
R/ASpli_show_methods.R
R/DUreport_functions.R
R/binGenome_functions.R
R/bins_DEXSeq.R
R/loadBam_function.R
R/plotTopTags_function.R
R/readCounts_functions.R
build
build/vignette.rds
inst
inst/NEWS
inst/doc
inst/doc/ASpli.R
inst/doc/ASpli.Rnw
inst/doc/ASpli.pdf
inst/extdata
inst/extdata/chr14.sqlite
man
man/ASpli-package.Rd
man/ASpliAS-class.Rd
man/ASpliCounts-class.Rd
man/ASpliCounts.Rd
man/ASpliDU-class.Rd
man/ASpliFeatures-class.Rd
man/AsDiscover-methods.Rd
man/DUreport.Rd
man/DUreport_DEXSeq.Rd
man/acc_AS.Rd
man/acc_DU.Rd
man/acc_counts.Rd
man/acc_features.Rd
man/binGenome-methods.Rd
man/binGenome.Rd
man/loadBAM.Rd
man/plotTopTags.Rd
man/rds.Rd
man/readCounts.Rd
man/show-methods.Rd
man/write-methods.Rd
man/write.Rd
vignettes
vignettes/ASpli.Rnw
vignettes/ASpli.bib
vignettes/LRR1_E005.png
vignettes/binDefinition.png
vignettes/pir.png
vignettes/psi_altSS.png
vignettes/psi_es.png
vignettes/venn.png
vignettes/wf.png
ASpli documentation built on May 20, 2017, 9:21 p.m.