InPAS: Identification of Novel alternative PolyAdenylation Sites (PAS)
Version 1.8.0

Alternative polyadenylation (APA) is one of the important post-transcriptional regulation mechanisms which occurs in most human genes. InPAS facilitates the discovery of novel APA sites from RNAseq data. It leverages cleanUpdTSeq to fine tune identified APA sites.

AuthorJianhong Ou, Sung Mi Park, Michael R. Green and Lihua Julie Zhu
Bioconductor views AlternativeSplicing Coverage DifferentialSplicing GeneRegulation RNASeq Sequencing Transcription
Date of publicationNone
MaintainerJianhong Ou <jianhong.ou@umassmed.edu>, Lihua Julie Zhu <Julie.Zhu@umassmed.edu>
LicenseGPL (>= 2)
Version1.8.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("InPAS")

Getting started

Package overview
InPAS Vignette

Popular man pages

distalAdj: adjust distal CP sites by cleanUpdTSeq
filterRes: filter results
inPAS: do estimation of alternative polyadenylation and cleavage...
polishCPs: polish the searching results of CP sites
proximalAdj: adjust the proximal CP sites
totalCoverage: total coverage
utr3.mm10: 3'UTR annotation for mm10 obtained from utr3Annotation
See all...

All man pages Function index File listing

Man pages

coverageFromBedGraph: read coverage from bedGraph files
coverageRate: coverage rate of genes and 3UTRs
covThreshold: calculate the cutoff threshold of coverage
CPsite_estimation: estimate the cpsites
CPsites: predict the cleavage and polyadenylation(CP) site
depthWeight: calculate the depth weight for each example
distalAdj: adjust distal CP sites by cleanUpdTSeq
filterRes: filter results
fisher.exact.test: do fisher exact test for two group datasets
getCov: extract coverage from bedgraph file
get.regions.coverage: claculate coverage for giving region
getUTR3eSet: prepare dataset for test
getUTR3region: extract long and short 3UTR region
inPAS: do estimation of alternative polyadenylation and cleavage...
InPAS-package: alternative polyadenylation and cleavage estimations
lastCDSusage: extract coverage of last CDS exon region
limmaAnalyze: use limma to analyze the PDUI
optimalSegmentation: calculate SSE
PAscore: calculate the CP score
PAscore2: calculate the CP score
polishCPs: polish the searching results of CP sites
prepare4GSEA: prepare the files for GSEA analysis
proximalAdj: adjust the proximal CP sites
proximalAdjByCleanUpdTSeq: adjust the proximal CP sites by cleanUpdTseq
proximalAdjByPWM: adjust the proximal CP sites by PWM
removeUTR3__UTR3: remove the candicates LIKE UTR3___UTR3
searchDistalCPs: search distal CP sites
searchProximalCPs: search proximal CPsites
seqLen: get sequence lengths
singleGroupAnalyze: do analysis for single group samples
singleSampleAnalyze: do analysis for single sample
sortGR: sort GRanges
testUsage: do test for dPDUI
totalCoverage: total coverage
trimSeqnames: trim the sequence names
usage4plot: prepare coverage data and fitting data for plot
utr3Annotation: extract 3'UTR from TxDb object
UTR3eSet: Class 'UTR3eSet'
utr3.hg19: 3'UTR annotation for hg19 obtained from utr3Annotation
utr3.mm10: 3'UTR annotation for mm10 obtained from utr3Annotation
UTR3TotalCoverage: extract coverage of 3UTR for CP sites prediction
UTR3usage: calculate the usage of long and short form of UTR3
utr3UsageEstimation: estimation of 3'UTR usage for each region
valley: get the local minimal square standard error (SSE)
zScoreThrethold: calculate local background cutoff value

Functions

$,UTR3eSet-method Man page
$<-,UTR3eSet-method Man page
CPsite_estimation Man page Source code
CPsites Man page Source code
InPAS Man page
InPAS-package Man page
PAscore Man page Source code
PAscore2 Man page Source code
UTR3TotalCoverage Man page Source code
UTR3eSet Man page Source code
UTR3eSet-class Man page
UTR3usage Man page Source code
compensation Source code
covThreshold Man page Source code
coverageCDS Source code
coverageFromBedGraph Man page Source code
coverageRate Man page Source code
depthWeight Man page Source code
distalAdj Man page Source code
fft.smooth Source code
filterRes Man page Source code
fisher.exact.test Man page Source code
gcComp Source code
get.regions.coverage Man page Source code
getCov Man page Source code
getUTR3eSet Man page Source code
getUTR3region Man page Source code
inPAS Man page Source code
intronRegion Source code
lastCDSusage Man page Source code
limmaAnalyze Man page Source code
mapComp Source code
mergeCoverage Source code
optimalSegmentation Man page Source code
polishCPs Man page Source code
prepare4GSEA Man page Source code
proximalAdj Man page Source code
proximalAdjByCleanUpdTSeq Man page Source code
proximalAdjByPWM Man page Source code
removeTmpfile Source code
removeUTR3__UTR3 Man page Source code
searchDistalCPs Man page Source code
searchProximalCPs Man page Source code
seqLen Man page Source code
singleGroupAnalyze Man page Source code
singleSampleAnalyze Man page Source code
sortGR Man page Source code
testUsage Man page Source code
totalCoverage Man page Source code
trimSeqnames Man page Source code
usage4plot Man page Source code
utr3.hg19 Man page
utr3.mm10 Man page
utr3Annotation Man page Source code
utr3UsageEstimation Man page Source code
valley Man page Source code
zScoreThrethold Man page Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/CPsite_estimation.R
R/CPsites.R
R/Comp.R
R/PAscore.R
R/PAscore2.R
R/UTR3TotalCoverage.R
R/UTR3eSet.R
R/UTR3usage.R
R/covThreshold.R
R/coverageFromBedGraph.R
R/coverageRate.R
R/depthWeight.R
R/distalAdj.R
R/filterRes.R
R/fisher.exact.test.R
R/get.regions.coverage.R
R/getCov.R
R/getUTR3eSet.R
R/getUTR3region.R
R/inPAS.R
R/lastCDSusage.R
R/limmaAnalyze.R
R/mergeCoverage.R
R/optimalSegmentation.R
R/polishCPs.R
R/prepare4GSEA.R
R/proximalAdj.R
R/proximalAdjByCleanUpdTSeq.R
R/proximalAdjByPWM.R
R/removeUTR3__UTR3.R
R/searchDistalCPs.R
R/searchProximalCPs.R
R/seqLen.R
R/singleGroupAnalyze.R
R/singleSampleAnalyze.R
R/sortGR.R
R/testUsage.R
R/totalCoverage.R
R/trimSeqnames.R
R/usage4plot.R
R/utr3Annotation.R
R/utr3UsageEstimation.R
R/valley.R
R/zScoreThrethold.R
build
build/vignette.rds
data
data/datalist
data/utr3.hg19.rda
data/utr3.mm10.rda
inst
inst/doc
inst/doc/InPAS.R
inst/doc/InPAS.Rmd
inst/doc/InPAS.html
inst/extdata
inst/extdata/Baf3.extract.bedgraph
inst/extdata/CPs.MAQC.rda
inst/extdata/UM15.extract.bedgraph
inst/extdata/coverage.MAQC.rda
inst/extdata/eset.MAQC.rda
inst/extdata/polyA.rds
inst/unitTests
inst/unitTests/test_CPsites.R
inst/unitTests/test_coverageFromBedGraph.R
inst/unitTests/test_getUTR3eSet.R
man
man/CPsite_estimation.Rd
man/CPsites.Rd
man/InPAS-package.Rd
man/PAscore.Rd
man/PAscore2.Rd
man/UTR3TotalCoverage.Rd
man/UTR3eSet.Rd
man/UTR3usage.Rd
man/covThreshold.Rd
man/coverageFromBedGraph.Rd
man/coverageRate.Rd
man/depthWeight.Rd
man/distalAdj.Rd
man/filterRes.Rd
man/fisher.exact.test.Rd
man/get.regions.coverage.Rd
man/getCov.Rd
man/getUTR3eSet.Rd
man/getUTR3region.Rd
man/inPAS.Rd
man/lastCDSusage.Rd
man/limmaAnalyze.Rd
man/optimalSegmentation.Rd
man/polishCPs.Rd
man/prepare4GSEA.Rd
man/proximalAdj.Rd
man/proximalAdjByCleanUpdTSeq.Rd
man/proximalAdjByPWM.Rd
man/removeUTR3__UTR3.Rd
man/searchDistalCPs.Rd
man/searchProximalCPs.Rd
man/seqLen.Rd
man/singleGroupAnalyze.Rd
man/singleSampleAnalyze.Rd
man/sortGR.Rd
man/testUsage.Rd
man/totalCoverage.Rd
man/trimSeqnames.Rd
man/usage4plot.Rd
man/utr3.hg19.Rd
man/utr3.mm10.Rd
man/utr3Annotation.Rd
man/utr3UsageEstimation.Rd
man/valley.Rd
man/zScoreThrethold.Rd
tests
tests/runTests.R
vignettes
vignettes/InPAS.Rmd
InPAS documentation built on May 20, 2017, 10:57 p.m.

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