InPAS

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see InPAS.

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


Bioconductor version: 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 (!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 2.0.0
In Bioconductor since BioC 3.1 (R-3.2) (9 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
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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
Linking To
Enhances
Depends On Me
Imports Me
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Build Report 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
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 3.13 Source Archive