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 (!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

Details

biocViews AlternativeSplicing, Coverage, DifferentialSplicing, GeneRegulation, ImmunoOncology, RNASeq, Sequencing, Software, Transcription
Version 1.16.3
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
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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
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Build Report Build Report

Package Archives

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

Source Package InPAS_1.16.3.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
Bioc Package Browser https://code.bioconductor.org/browse/InPAS/
Package Short Url https://bioconductor.org/packages/InPAS/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive