To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("InPAS")
In most cases, you don't need to download the package archive at all.
InPAS
|
|
|
|
|
Identification of Novel alternative PolyAdenylation Sites (PAS)
Bioconductor version: Release (3.5)
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 from RNAseq data. It leverages cleanUpdTSeq to fine tune identified APA sites.
Author: Jianhong Ou, Sung Mi Park, Michael R. Green and Lihua Julie Zhu
Maintainer: Jianhong Ou <jianhong.ou at umassmed.edu>, Lihua Julie Zhu <Julie.Zhu at umassmed.edu>
Citation (from within R,
enter citation("InPAS")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("InPAS")
Documentation
| HTML | R Script | InPAS Vignette |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | AlternativeSplicing, Coverage, DifferentialSplicing, GeneRegulation, RNASeq, Sequencing, Software, Transcription |
| Version | 1.8.0 |
| In Bioconductor since | BioC 3.1 (R-3.2) (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 | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | InPAS_1.8.0.tar.gz |
| Windows Binary | InPAS_1.8.0.zip |
| Mac OS X 10.11 (El Capitan) | InPAS_1.8.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/InPAS |
| Package Short Url | http://bioconductor.org/packages/InPAS/ |
| Package Downloads Report | Download Stats |
Documentation »
Bioconductor
- Package vignettes and manuals.
- Workflows for learning and use.
- Course and conference material.
- Videos.
- Community resources and tutorials.
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations:
- Support site - for questions about Bioconductor packages
- Bioc-devel mailing list - for package developers
