Package: InPAS 2.15.0

Jianhong Ou

InPAS: Identify Novel Alternative PolyAdenylation Sites (PAS) from RNA-seq data

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 and the differential usage of APA sites from RNA-Seq data. It leverages cleanUpdTSeq to fine tune identified APA sites by removing false sites.

Authors:Jianhong Ou [aut, cre], Haibo Liu [aut], Lihua Julie Zhu [aut], Sungmi M. Park [aut], Michael R. Green [aut]

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InPAS.pdf |InPAS.html✨
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NEWS

# Install 'InPAS' in R:
install.packages('InPAS', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:

On BioConductor:InPAS-2.13.0(bioc 3.20)InPAS-2.12.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

alternative polyadenylationdifferential polyadenylation site usagerna-seqgene regulationtranscription

4.00 score 1 scripts 215 downloads 34 exports 137 dependencies

Last updated 23 days agofrom:45b2e2d34f. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winWARNINGOct 31 2024
R-4.5-linuxWARNINGOct 30 2024
R-4.4-winWARNINGOct 31 2024
R-4.4-macWARNINGOct 31 2024
R-4.3-winWARNINGOct 31 2024
R-4.3-macWARNINGOct 31 2024

Exports:addChr2ExcludeaddInPASEnsDbaddInPASGenomeaddInPASOutputDirectoryaddInPASTxDbaddLockNameassemble_allCovextract_UTR3Annofilter_testOutfind_minMSEDistrget_chromosomesget_lastCDSUTR3get_regionCovget_ssRleCovget_usage4plotget_UTR3eSetgetChr2ExcludegetInPASEnsDbgetInPASGenomegetInPASOutputDirectorygetInPASSQLiteDbgetInPASTxDbgetLockNameparse_TxDbplot_utr3Usagerun_coverageQCrun_limmaAnalysissearch_CPsset_globalssetup_CPsSearchsetup_GSEAsetup_parCPsSearchsetup_sqlitedbtest_dPDUI

Dependencies:abindade4AnnotationDbiaskpassbackportsbase64urlbatchtoolsBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobbrewBSgenomeBSgenome.Drerio.UCSC.danRer7cachemcheckmateclasscleanUpdTSeqclicliprcodetoolscolorspacecpp11crayoncurldata.tableDBIDelayedArraydepmixS4digestdplyre1071fansifarverfastmapflockformatRfsfutile.loggerfutile.optionsfuturefuture.applygenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2globalsgluegtablehmshttrIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecyclelimmalistenvmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmennetopensslparallellypillarpixmappkgconfigplogrplyrplyrangespngpreprocessCoreprettyunitsprogressproxyR6rappdirsRColorBrewerRcppRcppArmadilloRCurlreadrreshape2restfulrRhtslibrjsonrlangRsamtoolsRsolnpRSQLitertracklayerS4ArraysS4VectorsscalessegmentedseqinrsnowspSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyselecttruncnormtzdbUCSC.utilsutf8vctrsviridisLitevroomwithrXMLXVectoryamlzlibbioc

InPAS Vignette

Jianhong Ou, Haibo Liu, Sungmi Park, Michael Green, Lihua Julie Zhu

Rendered fromInPAS.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2022-03-29
Started: 2015-10-06

Readme and manuals

Help Manual

Help pageTopics
Add a globally-applied requirement for filtering out scaffolds from all analysisaddChr2Exclude
Add a globally defined EnsDb to some InPAS functions.addInPASEnsDb
Add a globally defined genome to all InPAS functions.addInPASGenome
Add a globally defined output directory to some InPAS functions.addInPASOutputDirectory
Add a globally defined TxDb for InPAS functions.addInPASTxDb
Add a filename for locking a SQLite databaseaddLockName
Assemble coverage files for a given chromosome for all samplesassemble_allCov
extract 3' UTR information from a GenomicFeatures::TxDb objectextract_UTR3Anno
filter 3' UTR usage test resultsfilter_testOut
Visualization of MSE profiles, 3' UTR coverage and minimal MSE distributionfind_minMSEDistr
Identify chromosomes/scaffolds for CP site discoveryget_chromosomes
Extract the last unspliced region of each transcriptget_lastCDSUTR3
Get coverage for 3' UTR and last CDS regions on a single chromosomeget_regionCov
Get Rle coverage from a bedgraph file for a sampleget_ssRleCov
prepare coverage data and fitting data for plotget_usage4plot
prepare 3' UTR coverage data for usage testget_UTR3eSet
Get a globally-applied requirement for filtering scaffolds.getChr2Exclude
Get the globally defined EnsDb.getInPASEnsDb
Get the globally defined genomegetInPASGenome
Get the path to a output directory for InPAS analysisgetInPASOutputDirectory
Get the path to an SQLite databasegetInPASSQLiteDb
Get the globally defined TxDb.getInPASTxDb
Get the path to a file for locking the SQLite databasegetLockName
A package for identifying novel Alternative PolyAdenylation Sites (PAS) based on RNA-seq dataInPAS
Extract gene models from a TxDb objectparse_TxDb
Visualize the dPDUI events using ggplot2plot_utr3Usage
Quality control on read coverage over gene bodies and 3UTRsrun_coverageQC
Estimate the CP sites for UTRs on a given chromosomesearch_CPs
Set up global variables for an InPAS analysisset_globals
prepare data for predicting cleavage and polyadenylation (CP) sitessetup_CPsSearch
prepare files for GSEA analysissetup_GSEA
Prepare data for predicting cleavage and polyadenylation (CP) sites using parallel computingsetup_parCPsSearch
Create an SQLite database for storing metadata and paths to coverage filessetup_sqlitedb
do test for dPDUItest_dPDUI
Annotation of 3' UTRs for mouse (mm10)utr3.mm10
UTR3eSet-class and its methods$,UTR3eSet-method $<-,UTR3eSet-method coerce,UTR3eSet,ExpressionSet-method coerce,UTR3eSet,GRanges-method show,UTR3eSet-method UTR3eSet-class