Estimate Promoter Activity from RNA-Seq data (original) (raw)
Release History
Release 1.1.18
Date: 7th April 2021
Changes in version 1.1.18:
- Gene expression data is now stored in the
assays
of the summarizedExperiment object returned byproActiv
to facilitate easier filtering of the summarizedExperiment object. The metadata slot is now empty. - Plotting promoter activity: Implementation of
boxplotPromoters
function to plot boxplots of absolute promoter activity, relative promoter activity, and gene expression. - Identification of alternative promoters: Implementation of
getAlternativePromoters
, used to identify promoters that may exhibit alternative usage.
Release 1.0.0
Release date: 28th October 2020
Released with Bioconductor 3.12
Release 0.99.0
Release date: 21st August 2020
Changes in version 0.99.0:
- Workflow: The wrapper function
proActiv
performs all steps to estimate promoter activity and calculates promoter metadata. Acondition
argument can be supplied forproActiv
to summarize promoter counts and activity across conditions. These results are returned as a SummarizedExperiment object. - BAM file usage: In addition to junction files,
proActiv
now allows BAM files as input. However, users should note that this function is not fully optimized and may have long run-time. - Promoter annotation: Improved efficiency in generating promoter annotations without the need for parallelization with the
preparePromoterAnnotations
function. The promoter annotation object is also trimmed to preserve essential information for runningproActiv
, in order to comply with Bioconductor guidelines concerning package size. - Plotting promoter activity: The plotting function
plotPromoters
visualizes promoter activity across conditions. It accepts the SummarizedExperiment object returned byproActiv
along with a gene of interest and gene annotations as arguments. This allows users to visualize promoter activity and identify instances of alternative promoter usage. - Vignette: proActiv now comes with a vignette, documenting a complete step-by-step workflow in identifying active and alternative promoter usage. This includes guidance on running
proActiv
, creating promoter annotations and identifying alternative promoter usage. Various visualizations of promoter activity are also offered.
Initial Release 0.1.0
Release date: 19th May 2020
This release corresponds to the proActiv version used by Demircioglu et al.
Limitations
proActiv will not provide promoter activity estimates for promoters which are not uniquely identifiable from splice junctions (single exon transcripts, promoters which overlap with internal exons).