InPAS: Identification of Novel alternative PolyAdenylation Sites (PAS)

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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.

Author
Jianhong Ou, Sung Mi Park, Michael R. Green and Lihua Julie Zhu
Date of publication
None
Maintainer
Jianhong Ou <jianhong.ou@umassmed.edu>
License
GPL (>= 2)
Version
1.6.0

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

Files in this package

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