InPAS
This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see InPAS.
A Bioconductor package for identifying novel Alternative PolyAdenylation Sites (PAS) from RNA-seq data
Bioconductor version: 3.13
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 "4.1") 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 | 2.0.0 |
| In Bioconductor since | BioC 3.1 (R-3.2) (9 years) |
| License | GPL (>= 2) |
| Depends | R (>= 3.1), methods, Biobase, GenomicRanges, S4Vectors |
| Imports | AnnotationDbi, BSgenome, cleanUpdTSeq, preprocessCore, IRanges, GenomeInfoDb, depmixS4, limma, BiocParallel, Biostrings, dplyr, magrittr, plyranges, readr, RSQLite, DBI, purrr, GenomicFeatures, ggplot2, reshape2 |
| System Requirements | |
| URL |
See More
| Suggests | RUnit, BiocGenerics, BiocManager, rtracklayer, BiocStyle, knitr, markdown, rmarkdown, EnsDb.Hsapiens.v86, EnsDb.Mmusculus.v79, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10, 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_2.0.0.tar.gz |
| Windows Binary | InPAS_2.0.0.zip (32- & 64-bit) |
| macOS 10.13 (High Sierra) | InPAS_2.0.0.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 3.13 | Source Archive |