To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

InPAS

 

Identification of Novel alternative PolyAdenylation Sites (PAS)

Bioconductor version: Release (3.5)

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>

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

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 1.8.0
In Bioconductor since BioC 3.1 (R-3.2) (2.5 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
Build Report  

Package Archives

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

Package Source InPAS_1.8.0.tar.gz
Windows Binary InPAS_1.8.0.zip
Mac OS X 10.11 (El Capitan) InPAS_1.8.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/InPAS
Package Short Url http://bioconductor.org/packages/InPAS/
Package Downloads Report Download Stats

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