Custom Shiny applications

For more interactive accessibility, our platform also develops custom R Shiny applications to make complex results easy to explore, share and reuse. We handle prototyping, development, secure deployment and maintenance, with a focus on reproducibility, documentation and sustainability.

What we offer

• Requirements gathering (target users, key questions, priorities)
• Exploration ‘portal’ functions (search, interactive graphics, cohort/cluster views, downloads)
• Analysis functions (filters, standardised comparisons, figure exports)
• Deployment design and production launch (internal hosting or approved cloud, performance optimisation)
• Documentation (user guide)
• Maintenance options (patches, dependency updates, functional upgrades)

What we need from you

• A brief description of the objectives and users (who the app is for and what decisions it should support)
• Representative data
• Access and security requirements (public/internal, roles if necessary)
• A scientific contact for quick validation during iterations

Example: BrainTime (Johanna Joyce Laboratory)

A common example is an application that serves as both an analysis tool and an exploration portal, allowing collaborators to verify results, compare groups and produce consistent figures. The BrainTIME application allows users to explore gene expression within immune populations in the microenvironment of human brain tumours, with interactive filters and standardised comparisons.

Submission to a database

We assist you in submitting your datasets to suitable hosting databases, such as GEO, SRA/ENA, ArrayExpress, Zenodo/Figshare, ensuring the quality of the metadata. We cannot guarantee final acceptance by the repository, but we maximise the compliance of the file.

What we offer

• Advice on choosing a host
• Help with metadata (study description, experimental design, sample annotations, protocols)
• Preparation of the ‘Data availability’ text for manuscripts and monitoring of accessions/embargoes

What we need from you

• The final files to be deposited (raw and/or processed depending on the repository) and a description of the pipeline if it has not been carried out by the BDSF platform
• A sample annotation table (and coding rules/abbreviations)
• Your schedule (submission before article submission, revision, acceptance)