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proActiv

Estimate Promoter Activity from RNA-Seq data


Bioconductor version: Release (3.18)

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. proActiv also allows visualization of promoter activity across conditions.

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

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

Citation (from within R, enter citation("proActiv")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("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")
Identifying Active and Alternative Promoters from RNA-Seq data with proActiv HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews AlternativeSplicing, DifferentialSplicing, Epigenetics, FunctionalGenomics, GeneExpression, GeneRegulation, Preprocessing, RNASeq, Software, Transcription, Transcriptomics
Version 1.12.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License MIT + file LICENSE
Depends R (>= 4.0.0)
Imports AnnotationDbi, BiocParallel, data.table, dplyr, DESeq2, IRanges, GenomicRanges, GenomicFeatures, GenomicAlignments, GenomeInfoDb, ggplot2, gplots, graphics, methods, rlang, scales, S4Vectors, SummarizedExperiment, stats, tibble
System Requirements
URL https://github.com/GoekeLab/proActiv
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Suggests testthat, rmarkdown, knitr, Rtsne, gridExtra
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Package Archives

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

Source Package proActiv_1.12.0.tar.gz
Windows Binary proActiv_1.12.0.zip
macOS Binary (x86_64) proActiv_1.12.0.tgz
macOS Binary (arm64) proActiv_1.12.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/proActiv
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/proActiv
Bioc Package Browser https://code.bioconductor.org/browse/proActiv/
Package Short Url https://bioconductor.org/packages/proActiv/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.18 Source Archive