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 by proActiv 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. A condition argument can be supplied for proActiv 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 running proActiv, 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 by proActiv 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).