InPAS

DOI: 10.18129/B9.bioc.InPAS  

Identify Novel Alternative PolyAdenylation Sites (PAS) from RNA-seq data

Bioconductor version: Release (3.16)

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.

Author: Jianhong Ou [aut, cre], Haibo Liu [aut], Lihua Julie Zhu [aut], Sungmi M. Park [aut], Michael R. Green [aut]

Maintainer: Jianhong Ou <jianhong.ou at duke.edu>

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

Installation

To install this package, start R (version "4.2") 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")

 

HTML R Script InPAS Vignette
PDF   Reference Manual
Text   NEWS

Details

biocViews Alternative Polyadenylation, Differential Polyadenylation Site Usage, Gene Regulation, RNA-seq, Software, Transcription
Version 2.6.0
In Bioconductor since BioC 3.1 (R-3.2) (8 years)
License GPL (>= 2)
Depends R (>= 3.5.0)
Imports AnnotationDbi, batchtools, Biobase, Biostrings, BSgenome, cleanUpdTSeq, depmixS4, dplyr, flock, future, future.apply, GenomeInfoDb, GenomicRanges, GenomicFeatures, ggplot2, IRanges, limma, magrittr, methods, parallelly, plyranges, preprocessCore, readr, reshape2, RSQLite, stats, S4Vectors, utils
LinkingTo
Suggests BiocGenerics, BiocManager, BiocStyle, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Hsapiens.UCSC.hg19, EnsDb.Hsapiens.v86, EnsDb.Mmusculus.v79, knitr, markdown, rmarkdown, rtracklayer, RUnit, grDevices, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
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Build Report  

Package Archives

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

Source Package InPAS_2.6.0.tar.gz
Windows Binary InPAS_2.6.0.zip
macOS Binary (x86_64) InPAS_2.6.0.tgz
macOS Binary (arm64) InPAS_2.6.0.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

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