InPAS
Identify Novel Alternative PolyAdenylation Sites (PAS) from RNA-seq data
Bioconductor version: Release (3.17)
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("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 | ||
| NEWS | Text |
Details
| biocViews | Alternative Polyadenylation, Differential Polyadenylation Site Usage, Gene Regulation, RNA-seq, Software, Transcription |
| Version | 2.8.0 |
| In Bioconductor since | BioC 3.1 (R-3.2) (8.5 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 |
| Linking To | |
| 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 |
| System Requirements | |
| Enhances | |
| URL |
See More
| 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_2.8.0.tar.gz |
| Windows Binary | InPAS_2.8.0.zip |
| macOS Binary (x86_64) | InPAS_2.8.0.tgz |
| macOS Binary (arm64) | InPAS_2.8.0.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 |