Version 1.4.0

This release includes a number of updates to documentation, backend maintenance, and updates to the frontend app:

• Changed link to new sample result cache file
• Version increment for GenomicDistrubtions dependency
• Frontend app now displays LOLAweb version in footer instead of most recent commit hash
• Environment variables specifying reference data directories are now passed to the app more reliably (i.e., using file.path() instead of paste0() to construct path)
• Documentation overhaul for LOLAweb Docker instructions
• Backend changes to use GitHub Actions for continuous integration on production/development instances

Version 1.3.1

This releases fixes a bug in LOLAweb sample results and adds to documentation:

• Changed link to new sample result cache file
• Added badge for Docker builds to readme

Version 1.3.0

This release introduces several new LOLAweb features and enhancements:

• New button to download all plots in single .zip file
• Standardized text size and style in plots
• Fixed aspect ratios for plots
• Updated citation information in the about section

Version 1.2.2

minor release for LOLAweb resolving bugs:

• missing Google Analytics tracking code

Version 1.2.1

Minor release of LOLAweb to resolve bugs with:

• mm9 data not being available in GenomicDistributions
• barplot sorting
• run summary table not displaying as expected

LOLAweb 1.2

LOLAweb version 1.2 introduces a number of new features:

• Processed data now displays interactive scatter plot
• Results panel has been divided into tabs for scatter plot, barplots, distribution plots, table and run summary statistics
• Barplots limited to 50 results at most
• Barplot axis labels re-sized based on number of results
• Enhanced documentation in tooltips
• Major changes to structure and content on the documentation in the About page
• New reference genome (mm9) added
• Option added to build restricted universe based on input region sets
• Example data choices expanded and now pre-populated based on reference genome selected
• Universes available now pre-populated by reference genome selected

LOLAweb 1.1.1

Releasing LOLAweb version 1.1.1 to accommodate some minor bug fixes:

• .bed files are now loaded using readBed() instead of read.table()
• the current commit hash (linked to commit on Github) now included in footer
• fixes a bug that showed example results even for a user-uploaded query set

LOLAweb 1.1

The v1.1 release of LOLAweb includes new navigation features, an additional plot, and more help text:

• The app now uses a menu bar layout with tabs forrun, results and about tabs
• The results window includes a plot for distance to transcription start sites (TSS)
• The about page has been added to provide general information about using LOLAweb, as well as guidance on cache retention and how to share cached results

LOLAweb 1.0

This is the initial release of LOLAweb, an interactive application for enrichment analysis of genomic locus overlaps. The app is written in R using the Shiny framework, and is hosted via open-source Shiny server in a Docker container environment.

LOLAweb provides:

• an interface for uploading user-specific region sets, and selecting annotated region databases
• interactive visualizations of significant overlapping regions
• exploratory plots of distributions of genomic regions being queried across genome
• cached results allowing users to share or revisit without re-running computations

The application is available at http://lolaweb.databio.org

More features coming soon ... 🚀