InPAS

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

Bioconductor version: Release (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	2.14.0
In Bioconductor since	BioC 3.1 (R-3.2) (9.5 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
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_2.14.0.tar.gz
Windows Binary (x86_64)	InPAS_2.14.0.zip (64-bit only)
macOS Binary (x86_64)	InPAS_2.14.0.tgz
macOS Binary (arm64)	InPAS_2.13.0.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