Bioconductor - InPAS

Bioconductor - InPAS
Bioconductor 3.22
Software Packages
InPAS
InPAS
This is the
released
version of InPAS; for the devel version, see
InPAS
Identify Novel Alternative PolyAdenylation Sites (PAS) from RNA-seq data
DOI:
10.18129/B9.bioc.InPAS
Bioconductor version:
Release (3.22)
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
Citation (from within R, enter
citation("InPAS")
):
Installation
To install this package, start R (version "4.5") 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
PDF
NEWS
Text
Need some help? Ask on the Bioconductor Support site!
Details
biocViews
Alternative Polyadenylation
Differential Polyadenylation Site Usage
Gene Regulation
RNA-seq
Software
Transcription
Version
2.18.1
In Bioconductor since
BioC 3.1 (R-3.2) (11 years)
License
GPL (>= 2)
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
System Requirements
URL
See More
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
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_2.18.1.tar.gz
Windows Binary (x86_64)
InPAS_2.18.1.zip
macOS Binary (x86_64)
InPAS_2.18.1.tgz
macOS Binary (arm64)
InPAS_2.18.1.tgz
Source Repository
git clone https://git.bioconductor.org/packages/InPAS
Source Repository (Developer Access)
git clone git@git.bioconductor.org:packages/InPAS
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