proActiv
This is the development version of proActiv; for the stable release version, see proActiv.
Estimate Promoter Activity from RNA-Seq data
Bioconductor version: Development (3.21)
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] (ORCID:
Maintainer: Joseph Lee <joseph.lee at u.nus.edu>
citation("proActiv")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 |
Details
| biocViews | AlternativeSplicing, DifferentialSplicing, Epigenetics, FunctionalGenomics, GeneExpression, GeneRegulation, Preprocessing, RNASeq, Software, Transcription, Transcriptomics |
| Version | 1.17.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (4 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, txdbmaker |
| System Requirements | |
| URL | https://github.com/GoekeLab/proActiv |
See More
| Suggests | testthat, rmarkdown, knitr, Rtsne, gridExtra |
| 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 | proActiv_1.17.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 |