InPAS

This package is for version 3.20 of Bioconductor; for the stable, up-to-date release version, see InPAS.

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

Bioconductor version: 3.20

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.

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

Maintainer: Jianhong Ou <jianhong.ou at duke.edu>

Citation (from within R, enter citation("InPAS")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("InPAS")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("InPAS")

InPAS Vignette HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Alternative Polyadenylation, Differential Polyadenylation Site Usage, Gene Regulation, RNA-seq, Software, Transcription

Version 2.14.1

In Bioconductor since BioC 3.1 (R-3.2) (10 years)

License GPL (>= 2)

Depends R (>= 3.5.0)

Imports AnnotationDbi, batchtools, Biobase, Biostrings, BSgenome, cleanUpdTSeq, depmixS4, dplyr, flock, future, future.apply, GenomeInfoDb, GenomicRanges, GenomicFeatures, ggplot2, IRanges, limma, magrittr, methods, parallelly, plyranges, preprocessCore, readr, reshape2, RSQLite, stats, S4Vectors, utils

System Requirements

URL

Suggests BiocGenerics, BiocManager, BiocStyle, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Hsapiens.UCSC.hg19, EnsDb.Hsapiens.v86, EnsDb.Mmusculus.v79, knitr, markdown, rmarkdown, rtracklayer, RUnit, grDevices, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene

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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package InPAS_2.14.1.tar.gz

Windows Binary (x86_64) InPAS_2.14.1.zip (64-bit only)

macOS Binary (x86_64) InPAS_2.14.1.tgz

macOS Binary (arm64) InPAS_2.14.1.tgz

Source Repository git clone https://git.bioconductor.org/packages/InPAS

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/InPAS

Bioc Package Browser https://code.bioconductor.org/browse/InPAS/

Package Short Url https://bioconductor.org/packages/InPAS/

Package Downloads Report Download Stats

Old Source Packages for BioC 3.20 Source Archive