InPAS: Identification of Novel alternative PolyAdenylation Sites (PAS)

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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("InPAS")
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>
LicenseGPL (>= 2)
Version1.6.0

View on Bioconductor

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

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

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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