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>

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

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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: