bioinfoRmatics

The next R meetup is coming up in October with exciting topics from bioinformatics and life sciences, and I am very much looking forward to meeting you all!

• Although we already have 6 lighting talks scheduled, if you are interested in giving a 5-15 mins talk (freestyle, either in Hungarian or English), please let us know.
• If you are not willing to speak this time -- no worries; please join us for the talks and the networking event afterward.

Schedule:

• 18:00 doors open
• 18:15 6 talks (10 mins + few mins Q&A each)
• 19:30 networking (pizza, soft drinks)
• 20:30 end of meetup, optionally walking to a nearby pub

List of planned talks:

• Rádai Zoltán: Overcoming the performance-hurdle via parallelization

In comparison to other high-level languages (e.g. python or julia), R has an infamously poor performance in iterative tasks. Fortunately though, some powerful packages are available that make parallelization in iterative tasks relatively simple, providing a substantial performance boost even on mid-grade desktop PCs and laptops, with substantial utility in the analyses of biological data.

• Eszter Ari (Bioinformatician Researcher @ Biological Research Centre Szeged, University Teacher @ ELTE): MulEA - An R Package for Multi-Enrichment Analysis

MulEA is a comprehensive overrepresentation and functional enrichment analyser R package, which provides extensive analytical capabilities using a variety of ontologies, two distinct statistical models, and an empirical p-value correction procedure. MulEA allows us to extend our understanding of the results of various high-throughput analyses, such as genomics, transcriptomics, or proteomics. [abstract truncated]

• Póti Ádám (Természettudományi Kutatóközpont, Genomstabilitás Kutatócsoport, Budapest): Mutációs folyamatok felderítése R segítségével

Az elmúlt évtizedben nagyon sikeres módszertan épült ki arra, hogy tumorok teljesgenom-szekvenálási adataiból kimutatható legyen, hogy milyen károsító hatások érték az adott szövetet. A kutatócsoportban, ahol dolgozom, ezeket folyamatokat modellezzük különböző DNS-károsító szerekkel kezelt, illetve a genomstabilitásban fontos génekre mutáns sejtkultúrák segítségével. Előadásomban azt mutatnám be, hogy a gyakorlatban hogyan végezzük a mutációs adatok kiértékelését a megfelelő R-csomagok segítségével.

• Tyler Teadora (PhD student @ Anatomy Department of Semmelweis University, single cell RNA sequencing projects @ Data Science & Me): ShinyCell - a shiny package for single cell RNA sequencing data

Single cell RNA sequencing produces heaps of data that needs to be handled. While analyzing it, one often ends up with hundreds of very similar, slightly different plots. How to present these without making everyones eyes water? For example, with the ShinyCell package.

• Oláh Gergő (Debreceni Egyetem, Evolúciós Állattani és Humánbiológiai Tanszék): OBM-Insight - Using Rshiny for understanding biological data

OBM-Insight is an RShiny-based application that allows OpenBioMaps users to explore and analyse the data in their databases. It is a standalone application that can be used individually or as a free service and can connect to any known OpenBioMaps instance. The application retrieves data from remote PostgreSQL databases for the user via a database connection through the OpenBioMaps API. [abstract truncated]

• Gergely Daróczi (Co-founder and CTO of Rx Studio): Beyond Shiny: an R-based Precision Dosing Web Application

Shiny was a game-changer for many R developers, making it possible to publish stand-alone web applications written in R, but it is not always straightforward how to customize, scale, integrate in other applications, not to mention internationalization or regulatory issues. This talk provides a quick overview on the design considerations and the actual infrastructure behind Rx Studio, a precision dosing web and EHR application, using R to define the frontend elements, taking care of localization/i18n, and running MCMC simulations using PK/PD models.

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This is a joint meetup with R Ladies Budapest, co-organized with DS&ME, and kindly hosted by CEU. Food (pizza) and drinks will be served onsite after the talks, and we will also make table reservations in a nearby pub after 9.00 pm.