proActiv v0.99.0

This release corresponds to the Bioconductor pre-release version of proActiv.
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. Promoter annotation objects for human (hg19/hg38) and mouse (mm9/mm10) genomes are now pre-calculated and available to the user. 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.