InPAS
This is thereleased version of InPAS; for the devel version, seeInPAS.
Identify Novel Alternative PolyAdenylation Sites (PAS) from RNA-seq data
Bioconductor version: Release (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("InPAS")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("InPAS")For older versions of R, please refer to the appropriateBioconductor 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 | 2.18.1 |
| In Bioconductor since | BioC 3.1 (R-3.2) (10.5 years) |
| License | GPL (>= 2) |
| 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 |
| 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
FollowInstallation instructions to use this package in your R session.
| Source Package | InPAS_2.18.1.tar.gz |
| Windows Binary (x86_64) | InPAS_2.18.0.zip |
| macOS Binary (x86_64) | InPAS_2.18.1.tgz |
| macOS Binary (arm64) | InPAS_2.18.1.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 |
| Old Source Packages for BioC 3.22 | Source Archive |