InPAS
Identify Novel Alternative PolyAdenylation Sites (PAS) from RNA-seq data
Bioconductor version: 3.23 · Package version: 2.20.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("InPAS")Details
| Maintainer | Jianhong Ou <jou@morgridge.org> |
| Author | Jianhong Ou [aut, cre], Haibo Liu [aut], Lihua Julie Zhu [aut], Sungmi M. Park [aut], Michael R. Green [aut] |
| License | GPL (>= 2) |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Alternative Polyadenylation, Differential Polyadenylation Site Usage, Gene Regulation, RNA-seq, Software, Transcription |
| Package Short Url | https://bioconductor.org/packages/InPAS/ |
Citation
From within R, enter citation("InPAS"):
Jianhong Ou, Haibo Liu, Lihua Julie Zhu, Sungmi M. Park, Michael R. Green. InPAS: Identify Novel Alternative PolyAdenylation Sites (PAS) from RNA-seq data. doi:10.18129/B9.bioc.InPAS, R package version 2.20.0, https://bioconductor.org/packages/InPAS.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | InPAS_2.20.0.tar.gz |
| Windows binary (x86_64) | InPAS_2.20.0.zip |
| macOS binary (arm64) | InPAS_2.20.0.tgz |
| macOS binary (x86_64) | InPAS_2.20.0.tgz |
Dependencies
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
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