InPAS

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see InPAS.

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


Bioconductor version: 3.17

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 "4.3") 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

Details

biocViews Alternative Polyadenylation, Differential Polyadenylation Site Usage, Gene Regulation, RNA-seq, Software, Transcription
Version 2.8.0
In Bioconductor since BioC 3.1 (R-3.2) (9 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
See More
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
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package InPAS_2.8.0.tar.gz
Windows Binary InPAS_2.8.0.zip
macOS Binary (x86_64) InPAS_2.8.0.tgz
macOS Binary (arm64) InPAS_2.8.0.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 3.17 Source Archive