InPAS
This is the released version of InPAS; for the devel version, see InPAS.
All Bioconductor versions of InPAS
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1
Identify Novel Alternative PolyAdenylation Sites (PAS) from RNA-seq data
Bioconductor version: 3.23 · Package version: 2.20.0
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"):
Jianhong Ou, Haibo Liu, Lihua Julie Zhu, Sungmi M. Park, Michael R. Green. InPAS: Identify Novel Alternative PolyAdenylation Sites (PAS) from RNA-seq data. doi:10.18129/B9.bioc.InPAS, R package version 2.20.0, https://bioconductor.org/packages/InPAS.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") 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.
Details
| Version | 2.20.0 |
| License | GPL (>= 2) |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.1 (R-3.2) (11 years) |
| Downloads rank | 465 of 2,418 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Alternative Polyadenylation, Differential Polyadenylation Site Usage, Gene Regulation, RNA-seq, Software, Transcription |
| Package Short Url | https://bioconductor.org/packages/InPAS/ |
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 | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | InPAS_2.20.0.tar.gz |
| Windows binary (x86_64) | InPAS_2.20.0.zip |
| macOS binary (arm64) | InPAS_2.20.0.tgz |
| macOS binary (x86_64) | InPAS_2.20.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/InPAS |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/InPAS |
| Package Downloads Report | Download Stats |
Dependencies
Depends: R (>= 3.5)
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, Seqinfo, stats, S4Vectors, utils
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