useR! 2024: Full Schedule

In Person
8 - 11 July, 2024
Learn more and Register to Attend

The Sched app allows you to build your schedule but is not a substitute for your event registration. You must be registered for useR! 2024 to participate in the sessions. If you have not registered but would like to join us, please go to the event registration page to purchase a registration.

Please note: This schedule is automatically displayed in Central European Summer Time (UTC+02:00). To see the schedule in your preferred timezone, please select from the drop-down located at the bottom of the menu to the right.

IMPORTANT NOTE: Timing of sessions and room locations are subject to change.

The virtual program will take place on 2 July. Please see the virtual schedule page for more information.

13:30 CEST

Dupseqr: Disentangling Genomic Aberrations Made Easy - Ekaterina Akimova & Philine Hoven, Laboratory for Immunological and Molecular Cancer Research

Wednesday July 10, 2024 13:30 - 15:00 CEST

TBD

Aberrant repair of DNA double strand breaks is a prominent feature of various cancers. It can result in deletions, duplications, translocations and insertions. In our previous work, we analyzed amplicon-sequencing data with our custom pipeline to detect templated insertions at the DNA damage sites (Akimova et al. 2021, doi:10.1093/nar/gkab051). Here we present the dupseqr, an R package, which summarizes several functions for a sequential tracing of insertions, duplications and inversions. Dupseqr comprises, on the one hand, the existing bash commands in a pipe function for the pre-processing of the FASTQ files and BLAST search, followed by precise trimming and filtering of mapped sequences in order to identify insertions. On the other hand, it includes a novel function to detect and depict duplications and inversions directly from your DNA sequences, whereas the input and the output can be adjusted depending on your initial data structure and your final goal. All in all, dupseqr provides a quick possibility to elucidate aberrations, such as short duplications, inversions and insertions from distant genomic sites using the sequencing data.

Speakers

Ekaterina Akimova

Dr. rer. nat., Laboratory for Immunological and Molecular Cancer Research

I completed my PhD at LIMCR, investigating DNA damage in cancer. During this time, I worked on various projects, including the development of R-based analysis pipelines, and found my passion for coding. In 2023, I finished the doctorate, but continued my research endeavours as a PostDoc... Read More →

Philine Hoven

MSc, Laboratory for Immunological and Molecular Cancer Research

I am a PhD student of Natural and Life Sciences, currently working on the characterization of templated sequences insertions in the cancer background. My work involves wet lab techniques as well as data analytics with R.

Wednesday July 10, 2024 13:30 - 15:00 CEST
TBD

Biostatistics + epidemiology + bioinformatics, Poster Session

13:30 CEST

Exploring the Within-Individual Variability of Human Motor Learning Using GAMLSS - Julia Wood, The University of Queensland

Wednesday July 10, 2024 13:30 - 15:00 CEST

TBD

The neural correlates of learning are frequently explored in neuroscience research, typically through learning-induced changes in the mean of a response variable. Motor skill learning can enhance neural communication between the brain and the trained muscle. This communication is typically assessed by inducing muscle contractions in the trained pathway and measuring changes in mean size over time, with larger measurements suggesting enhanced communication. Motor learning may also improve the efficiency of this communication, possibly reflected by more consistent muscle contractions and a reduction in the within-individual variability of these measurements over time. This study explored how motor skill learning and a subsequent intervention (active vs. placebo) influenced changes in the mean size and within-individual variability of these measurements. Effects were estimated by fitting a location and scale model using the GAMLSS package in R. GAMLSS fits a distributional model, which can estimate all parameters for the specified distribution. The results and analysis pipeline from this study will be discussed, emphasising the utility of the GAMLSS model in this research.

Speakers

Julia Wood

Miss, The University of Queensland

After working as an R&D chemist for several years, I became intrigued by why we sleep and how we form new memories. This inspired me to pursue a doctoral path in human sleep and memory research. During my PhD, I have discovered deep interests in data analysis, statistical modelling... Read More →

Wednesday July 10, 2024 13:30 - 15:00 CEST
TBD

Biostatistics + epidemiology + bioinformatics, Poster Session

13:30 CEST

MINT+: Web App with R Brains for SDTM Automation - Magdalena Krochmal & Adam Forys, Roche

Wednesday July 10, 2024 13:30 - 15:00 CEST

TBD

In the realm of clinical research, a web application known as MINT+ is revolutionizing the process of SDTM automation. At its core, MINT+ utilizes a set of R-packages to power the entire solution. Its intuitive React UI empowers users to create custom SDTM mapping specifications, accommodating diverse study requirements. Leveraging DocumentDB for data storage, MINT+ enables easy metadata sharing and facilitates reuse across studies, significantly reducing workload and improving accuracy.
During this session, we will explore the R-based components that power MINT+ and are responsible for data processing and backend processes. The "rmint.sdtm" automates SDTM mappings, "rsaffron.api" serves as the backend API, and "roak" allows customization of mappings. Users can address complex scenarios that often arise in the SDTM mapping creation process, making R packages the preferred choice for overcoming industry challenges.
With advanced algorithms, a user-friendly interface, and seamless integration, MINT+ streamlines SDTM creation workflow, greatly reducing the time and effort required.

Speakers

Magdalena Krochmal

Senior Data Scientist, Roche

Magdalena Krochmal is a Senior Data Scientist based in Basel, Switzerland. With a background in biomedical engineering and a Ph.D. in bioinformatics, she has spent three impactful years at Roche. Magdalena is an expert R developer specializing in SDTM automation. Her work centers... Read More →

Adam Forys

Mr., Roche

Adam is a Principal Data Scientist at Roche. He is dedicated to building R packages that empower teams working on SDTM. He is committed to collaboration and enjoys guiding others in overcoming technical obstacles and optimizing their data science workflows.

Wednesday July 10, 2024 13:30 - 15:00 CEST
TBD

Biostatistics + epidemiology + bioinformatics, Poster Session

13:30 CEST

Use of R in Calibration of Infectious Disease Models - Nicole Swartwood, Harvard TH Chan School of Public Health

Wednesday July 10, 2024 13:30 - 15:00 CEST

TBD

Calibration approaches are commonly used in infectious disease modeling, but there has been little study to describe the use of these techniques within the field. Furthermore, R is increasingly used by epidemiologists to understand disease dynamics. As part of a larger scoping review investigating the distribution of calibration methods for models of HIV, TB, and malaria, we will collect data on programming languages and packages/libraries cited in published manuscripts. We aim to identify with which calibration strategies R is most commonly used and ultimately identify any gaps in and potential for development in the available calibration packages within R. We also aim to identify any association with disease, model goal, and or reducibility.

Speakers

Nicole Swartwood

Senior Research Analyst, Harvard TH Chan School of Public Health

Nicole Anne Swartwood is a infectious disease modeler at the Harvard TH Chan School of Public Health. Her work focuses on tuberculosis and COVID-19 in the United States. She co-founded the Harvard R User Group and remains as a co-organizer. She is passionate about empowering junior... Read More →

Wednesday July 10, 2024 13:30 - 15:00 CEST
TBD

Biostatistics + epidemiology + bioinformatics, Poster Session