proActiv

DOI: 10.18129/B9.bioc.proActiv    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see proActiv.

Estimate Promoter Activity from RNA-Seq data

Bioconductor version: 3.12

Most human genes have multiple promoters that control the expression of different isoforms. The use of these alternative promoters enables the regulation of isoform expression pre-transcriptionally. Alternative promoters have been found to be important in a wide number of cell types and diseases. proActiv is an R package that enables the analysis of promoters from RNA-seq data. proActiv uses aligned reads as input, and generates counts and normalized promoter activity estimates for each annotated promoter. In particular, proActiv accepts junction files from TopHat2 or STAR or BAM files as inputs. These estimates can then be used to identify which promoter is active, which promoter is inactive, and which promoters change their activity across conditions.

Author: Deniz Demircioglu [aut] , Jonathan Göke [aut], Joseph Lee [cre]

Maintainer: Joseph Lee <joseph.lee at u.nus.edu>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("proActiv")

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("proActiv")

 

HTML	R Script	Identifying Active and Alternative Promoters from RNA-Seq data with proActiv
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	AlternativeSplicing, DifferentialSplicing, Epigenetics, FunctionalGenomics, GeneExpression, GeneRegulation, Preprocessing, RNASeq, Software, Transcription, Transcriptomics
Version	1.0.0
In Bioconductor since	BioC 3.12 (R-4.0) (0.5 years)
License	MIT + file LICENSE
Depends	R (>= 4.0.0)
Imports	dplyr, GenomicRanges, GenomicFeatures, GenomicAlignments, GenomeInfoDb, IRanges, S4Vectors, methods, rlang, SummarizedExperiment, AnnotationDbi, DESeq2, data.table, tibble, Gviz, BiocParallel
LinkingTo
Suggests	testthat, mockery, BSgenome, BiocManager, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, DEXSeq, Rtsne, ggplot2, tidyr, vdiffr
SystemRequirements
Enhances
URL	https://github.com/GoekeLab/proActiv
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	proActiv_1.0.0.tar.gz
Windows Binary	proActiv_1.0.0.zip
macOS 10.13 (High Sierra)	proActiv_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/proActiv
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/proActiv
Package Short Url	https://bioconductor.org/packages/proActiv/
Package Downloads Report	Download Stats