InPAS

DOI: 10.18129/B9.bioc.InPAS    

A Bioconductor package for identifying novel Alternative PolyAdenylation Sites (PAS) from RNA-seq data

Bioconductor version: Release (3.13)

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>

Installation

To install this package, start R (version "4.1") 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	2.0.0
In Bioconductor since	BioC 3.1 (R-3.2) (6.5 years)
License	GPL (>= 2)
Depends	R (>= 3.1), methods, Biobase, GenomicRanges, S4Vectors
Imports	AnnotationDbi, BSgenome, cleanUpdTSeq, preprocessCore, IRanges, GenomeInfoDb, depmixS4, limma, BiocParallel, Biostrings, dplyr, magrittr, plyranges, readr, RSQLite, DBI, purrr, GenomicFeatures, ggplot2, reshape2
LinkingTo
Suggests	RUnit, BiocGenerics, BiocManager, rtracklayer, BiocStyle, knitr, markdown, rmarkdown, EnsDb.Hsapiens.v86, EnsDb.Mmusculus.v79, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene
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_2.0.0.tar.gz
Windows Binary	InPAS_2.0.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	InPAS_2.0.0.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