InPAS

DOI: 10.18129/B9.bioc.InPAS    

InPAS: a bioconductor package for the identification of novel alternative PolyAdenylation Sites (PAS) using RNA-seq data

Bioconductor version: Release (3.11)

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 due to internal-priming.

Author: Jianhong Ou, Sungmi M. Park, Michael R. Green and Lihua Julie Zhu

Maintainer: Jianhong Ou <jianhong.ou at duke.edu>, Lihua Julie Zhu <Julie.Zhu at umassmed.edu>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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")

 

HTML	R Script	InPAS Vignette
PDF		Reference Manual
Text		NEWS

Details

biocViews	AlternativeSplicing, Coverage, DifferentialSplicing, GeneRegulation, ImmunoOncology, RNASeq, Sequencing, Software, Transcription
Version	1.20.0
In Bioconductor since	BioC 3.1 (R-3.2) (5.5 years)
License	GPL (>= 2)
Depends	R (>= 3.1), methods, Biobase, GenomicRanges, GenomicFeatures, S4Vectors
Imports	AnnotationDbi, BSgenome, cleanUpdTSeq, Gviz, seqinr, preprocessCore, IRanges, GenomeInfoDb, depmixS4, limma, BiocParallel
LinkingTo
Suggests	RUnit, BiocGenerics, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10, org.Hs.eg.db, org.Mm.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, rtracklayer, knitr
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	InPAS_1.20.0.tar.gz
Windows Binary	InPAS_1.20.0.zip
macOS 10.13 (High Sierra)	InPAS_1.20.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/InPAS
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/InPAS
Package Short Url	https://bioconductor.org/packages/InPAS/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.11	Source Archive