DOI: 10.18129/B9.bioc.proActiv  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see proActiv.

Estimate Promoter Activity from RNA-Seq data

Bioconductor version: 3.16

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>

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biocViews AlternativeSplicing, DifferentialSplicing, Epigenetics, FunctionalGenomics, GeneExpression, GeneRegulation, Preprocessing, RNASeq, Software, Transcription, Transcriptomics
Version 1.8.0
In Bioconductor since BioC 3.12 (R-4.0) (2.5 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
Suggests testthat, rmarkdown, knitr, Rtsne, gridExtra
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