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Bioconductor - InPAS (development version)

InPAS

This is the development version of InPAS; for the stable release version, see InPAS.

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

Bioconductor version: Development (3.22)

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 <jou at morgridge.org>

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

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
Details biocViews Alternative Polyadenylation, Differential Polyadenylation Site Usage, Gene Regulation, RNA-seq, Software, Transcription Version 2.17.0 In Bioconductor since BioC 3.1 (R-3.2) (10 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 System Requirements URL See More 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 Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives

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

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