This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see InPAS.
Bioconductor version: 3.10
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 (from within R,
enter citation("InPAS")
):
To install this package, start R (version "3.6") and enter:
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("InPAS")
For older versions of R, please refer to the appropriate Bioconductor release.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("InPAS")
HTML | R Script | InPAS Vignette |
Reference Manual | ||
Text | NEWS |
biocViews | AlternativeSplicing, Coverage, DifferentialSplicing, GeneRegulation, ImmunoOncology, RNASeq, Sequencing, Software, Transcription |
Version | 1.18.0 |
In Bioconductor since | BioC 3.1 (R-3.2) (5 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 |
LinkingTo | |
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 |
SystemRequirements | |
Enhances | |
URL | |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | InPAS_1.18.0.tar.gz |
Windows Binary | InPAS_1.18.0.zip (32- & 64-bit) |
Mac OS X 10.11 (El Capitan) | InPAS_1.18.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/InPAS |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/InPAS |
Package Short Url | https://bioconductor.org/packages/InPAS/ |
Package Downloads Report | Download Stats |
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