proActiv
Estimate Promoter Activity from RNA-Seq data
Bioconductor version: 3.23 · Package version: 1.22.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("proActiv")Details
| Maintainer | Joseph Lee <joseph.lee@u.nus.edu> |
| Author | Deniz Demircioglu [aut] (ORCID: <https://orcid.org/0000-0001-7857-0407>), Jonathan Göke [aut], Joseph Lee [cre] |
| License | MIT + file LICENSE |
| URL | https://github.com/GoekeLab/proActiv |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | AlternativeSplicing, DifferentialSplicing, Epigenetics, FunctionalGenomics, GeneExpression, GeneRegulation, Preprocessing, RNASeq, Software, Transcription, Transcriptomics |
| Package Short Url | https://bioconductor.org/packages/proActiv/ |
Citation
From within R, enter citation("proActiv"):
Deniz Demircioglu, Jonathan Göke. proActiv: Estimate Promoter Activity from RNA-Seq data. doi:10.18129/B9.bioc.proActiv, R package version 1.22.0, https://bioconductor.org/packages/proActiv.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | proActiv_1.22.0.tar.gz |
| Windows binary (x86_64) | proActiv_1.22.0.zip |
| macOS binary (arm64) | proActiv_1.22.0.tgz |
| macOS binary (x86_64) | proActiv_1.22.0.tgz |
Dependencies
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
Suggests: GenomeInfoDbData, testthat, rmarkdown, knitr, Rtsne, gridExtra