InPAS

DOI: 10.18129/B9.bioc.InPAS    

Identification of Novel alternative PolyAdenylation Sites (PAS)

Bioconductor version: Release (3.6)

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 from RNAseq data. It leverages cleanUpdTSeq to fine tune identified APA sites.

Author: Jianhong Ou, Sung Mi Park, Michael R. Green and Lihua Julie Zhu

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("InPAS")

Documentation

HTML	R Script	InPAS Vignette
PDF		Reference Manual
Text		NEWS

Details

biocViews	AlternativeSplicing, Coverage, DifferentialSplicing, GeneRegulation, RNASeq, Sequencing, Software, Transcription
Version	1.10.0
In Bioconductor since	BioC 3.1 (R-3.2) (3 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
Build Report

Package Archives

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

Source Package	InPAS_1.10.0.tar.gz
Windows Binary	InPAS_1.10.0.zip
Mac OS X 10.11 (El Capitan)	InPAS_1.10.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/InPAS
Package Short Url	http://bioconductor.org/packages/InPAS/
Package Downloads Report	Download Stats