InPAS

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see InPAS.

Identification of Novel alternative PolyAdenylation Sites (PAS)

Bioconductor version: 3.7

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 (version "3.5") 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 AlternativeSplicing, Coverage, DifferentialSplicing, GeneRegulation, RNASeq, Sequencing, Software, Transcription

Version 1.12.0

In Bioconductor since BioC 3.1 (R-3.2) (9 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

System Requirements

URL

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

Linking To

Enhances

Depends On Me

Imports Me

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Build Report Build Report

Package Archives

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

Source Package InPAS_1.12.0.tar.gz

Windows Binary InPAS_1.12.0.zip

Mac OS X 10.11 (El Capitan) InPAS_1.12.0.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 3.7 Source Archive