InPAS

DOI: 10.18129/B9.bioc.InPAS    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see InPAS.

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

Bioconductor version: 3.9

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>

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

Installation

To install this package, start R (version "3.6") 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 1.16.3
In Bioconductor since BioC 3.1 (R-3.2) (4.5 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_1.16.3.tar.gz
Windows Binary InPAS_1.16.3.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) InPAS_1.16.3.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

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