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InPAS

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


Bioconductor version: Release (3.18)

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 "4.3") 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 Alternative Polyadenylation, Differential Polyadenylation Site Usage, Gene Regulation, RNA-seq, Software, Transcription
Version 2.10.0
In Bioconductor since BioC 3.1 (R-3.2) (9 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
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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
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Package Archives

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

Source Package InPAS_2.10.0.tar.gz
Windows Binary InPAS_2.10.0.zip (64-bit only)
macOS Binary (x86_64) InPAS_2.10.0.tgz
macOS Binary (arm64) InPAS_2.10.0.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