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 (3.20)
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 "4.4") 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")
InPAS Vignette | HTML | R Script |
Reference Manual | ||
NEWS | Text |
Details
biocViews | Alternative Polyadenylation, Differential Polyadenylation Site Usage, Gene Regulation, RNA-seq, Software, Transcription |
Version | 2.13.0 |
In Bioconductor since | BioC 3.1 (R-3.2) (9.5 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 |
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.
Source Package | InPAS_2.13.0.tar.gz |
Windows Binary | InPAS_2.13.0.zip |
macOS Binary (x86_64) | InPAS_2.13.0.tgz |
macOS Binary (arm64) | InPAS_2.13.0.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 |