Package: InPAS 2.21.0

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]

InPAS_2.21.0.tar.gz
InPAS_2.21.0.zip(r-4.7)InPAS_2.21.0.zip(r-4.6)InPAS_2.21.0.zip(r-4.5)
InPAS_2.21.0.tgz(r-4.6-any)InPAS_2.21.0.tgz(r-4.5-any)
InPAS_2.21.0.tar.gz(r-4.7-any)InPAS_2.21.0.tar.gz(r-4.6-any)
InPAS_2.21.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
InPAS/json (API)

# Install 'InPAS' in R:

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

Datasets:

utr3.mm10 - Annotation of 3' UTRs for mouse

On BioConductor:InPAS-2.21.0(bioc 3.24)InPAS-2.20.0(bioc 3.23)

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

alternative polyadenylation differential polyadenylation site usage rna-seq gene regulation transcription

4.30 score 2 scripts 577 downloads 34 exports 135 dependencies

Last updated from:15afd99d76. Checks:1 ERROR, 2 NOTE, 2 OK, 5 FAIL. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	500
linux-devel-x86_64	NOTE	774
source / vignettes	OK	507
linux-release-x86_64	NOTE	785
macos-release-arm64	FAIL	192
macos-oldrel-arm64	FAIL	182
windows-devel	FAIL	357
windows-release	FAIL	303
windows-oldrel	FAIL	306
wasm-release	OK	432

Exports:addChr2Exclude addInPASEnsDb addInPASGenome addInPASOutputDirectory addInPASTxDb addLockName assemble_allCov extract_UTR3Anno filter_testOut find_minMSEDistr get_chromosomes get_lastCDSUTR3 get_regionCov get_ssRleCov get_usage4plot get_UTR3eSet getChr2Exclude getInPASEnsDb getInPASGenome getInPASOutputDirectory getInPASSQLiteDb getInPASTxDb getLockName parse_TxDb plot_utr3Usage run_coverageQC run_limmaAnalysis search_CPs set_globals setup_CPsSearch setup_GSEA setup_parCPsSearch setup_sqlitedb test_dPDUI

Dependencies:abind ade4 AnnotationDbi askpass backports base64url batchtools BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob brew BSgenome BSgenome.Drerio.UCSC.danRer7 cachem checkmate cigarillo class cleanUpdTSeq cli clipr codetools cpp11 crayon curl data.table DBI DelayedArray depmixS4 digest dplyr e1071 farver fastmap flock formatR fs futile.logger futile.options future future.apply generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 globals glue gtable hms httr IRanges isoband jsonlite KEGGREST labeling lambda.r lattice lifecycle limma listenv magrittr MASS Matrix MatrixGenerics matrixStats memoise mime nlme nnet numDeriv openssl parallelly pillar pixmap pkgconfig plyr plyranges png preprocessCore prettyunits progress proxy R6 rappdirs RColorBrewer Rcpp RcppArmadillo RCurl readr reshape2 restfulr Rhtslib rjson rlang Rsamtools Rsolnp RSQLite rtracklayer S4Arrays S4Vectors S7 scales segmented Seqinfo seqinr snow sp SparseArray statmod stringi stringr SummarizedExperiment sys tibble tidyselect truncnorm tzdb UCSC.utils utf8 vctrs viridisLite vroom withr XML XVector yaml

InPAS Vignette

Rendered fromInPAS.Rmdusingknitr::rmarkdown

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

Help page	Topics
Add a globally-applied requirement for filtering out scaffolds from all analysis	addChr2Exclude
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 database	addLockName
Assemble coverage files for a given chromosome for all samples	assemble_allCov
extract 3' UTR information from a GenomicFeatures::TxDb object	extract_UTR3Anno
filter 3' UTR usage test results	filter_testOut
Visualization of MSE profiles, 3' UTR coverage and minimal MSE distribution	find_minMSEDistr
Identify chromosomes/scaffolds for CP site discovery	get_chromosomes
Extract the last unspliced region of each transcript	get_lastCDSUTR3
Get coverage for 3' UTR and last CDS regions on a single chromosome	get_regionCov
Get Rle coverage from a bedgraph file for a sample	get_ssRleCov
prepare coverage data and fitting data for plot	get_usage4plot
prepare 3' UTR coverage data for usage test	get_UTR3eSet
Get a globally-applied requirement for filtering scaffolds.	getChr2Exclude
Get the globally defined EnsDb.	getInPASEnsDb
Get the globally defined genome	getInPASGenome
Get the path to a output directory for InPAS analysis	getInPASOutputDirectory
Get the path to an SQLite database	getInPASSQLiteDb
Get the globally defined TxDb.	getInPASTxDb
Get the path to a file for locking the SQLite database	getLockName
A package for identifying novel Alternative PolyAdenylation Sites (PAS) based on RNA-seq data	-package InPAS
Extract gene models from a TxDb object	parse_TxDb
Visualize the dPDUI events using ggplot2	plot_utr3Usage
Quality control on read coverage over gene bodies and 3UTRs	run_coverageQC
Estimate the CP sites for UTRs on a given chromosome	search_CPs
Set up global variables for an InPAS analysis	set_globals
prepare data for predicting cleavage and polyadenylation (CP) sites	setup_CPsSearch
prepare files for GSEA analysis	setup_GSEA
Prepare data for predicting cleavage and polyadenylation (CP) sites using parallel computing	setup_parCPsSearch
Create an SQLite database for storing metadata and paths to coverage files	setup_sqlitedb
do test for dPDUI	test_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

Package: InPAS 2.21.0

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

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