InPAS
This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see InPAS.
InPAS: a bioconductor package for the identification of novel alternative PolyAdenylation Sites (PAS) using RNA-seq data
Bioconductor version: 3.12
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 due to internal-priming.
Author: Jianhong Ou, Sungmi M. Park, Michael R. Green and Lihua Julie Zhu
Maintainer: Jianhong Ou <jianhong.ou at duke.edu>, Lihua Julie Zhu <Julie.Zhu at umassmed.edu>
citation("InPAS")):
Installation
To install this package, start R (version "4.0") 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 | AlternativeSplicing, Coverage, DifferentialSplicing, GeneRegulation, ImmunoOncology, RNASeq, Sequencing, Software, Transcription |
| Version | 1.22.0 |
| In Bioconductor since | BioC 3.1 (R-3.2) (9 years) |
| License | GPL (>= 2) |
| Depends | R (>= 3.1), methods, Biobase, GenomicRanges, GenomicFeatures, S4Vectors |
| Imports | AnnotationDbi, BSgenome, cleanUpdTSeq, Gviz, seqinr, preprocessCore, IRanges, GenomeInfoDb, depmixS4, limma, BiocParallel |
| System Requirements | |
| URL |
See More
| Suggests | RUnit, BiocGenerics, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10, org.Hs.eg.db, org.Mm.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, rtracklayer, knitr |
| 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_1.22.0.tar.gz |
| Windows Binary | InPAS_1.22.0.zip |
| macOS 10.13 (High Sierra) | InPAS_1.22.0.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 |
| Old Source Packages for BioC 3.12 | Source Archive |