Related papers: MigraR: an open-source, R-based application for an…
Spectral line observations are an indispensable tool to remotely probe the physical and chemical conditions throughout the universe. Modelling their behaviour is a computational challenge that requires dedicated software. In this paper, we…
Statistics on migration flows are often derived from census data, which suffer from intrinsic limitations, including costs and infrequent sampling. When censuses are used, there is typically a time gap - up to a few years - between the data…
A lot of research relies on data analysis scripts to process, clean, and visualize data. However, recent studies show that these scripts are often hard to comprehend and maintain, hindering reproducibility and reuse, accompanied by a lack…
Cell migration is essential for regulating many biological processes in physiological or pathological conditions, including embryonic development and cancer invasion. In vitro and in silico studies suggest that collective cell migration is…
The package mvlearnR and accompanying Shiny App is intended for integrating data from multiple sources or views or modalities (e.g. genomics, proteomics, clinical and demographic data). Most existing software packages for multiview learning…
T cells undergo large shape changes (morphodynamics) when migrating. While progress has been made elucidating the molecular basis of cell migration, statistical characterization of morphodynamics and migration has been limited, particularly…
Interactive computing notebooks, such as Jupyter notebooks, have become a popular tool for developing and improving data-driven models. Such notebooks tend to be executed either in the user's own machine or in a cloud environment, having…
Motivation: The visualization and analysis of high-dimensional data are essential in biomedical research. There is a need for secure, scalable, and reproducible tools to facilitate data exploration and interpretation. Results: We introduce…
Summary: MALDIquant is an R package providing a complete and modular analysis pipeline for quantitative analysis of mass spectrometry data. MALDIquant is specifically designed with application in clinical diagnostics in mind and implements…
Tissue tracking plays a critical role in various surgical navigation and extended reality (XR) applications. While current methods trained on large synthetic datasets achieve high tracking accuracy and generalize well to endoscopic scenes,…
Microbiomes are a vital part of the human body, engaging in tasks like food digestion and immune defense. Their structure and function must be understood in order to promote host health and facilitate swift recovery during disease. Due to…
Summary: Mass spectrometry coupled to liquid chromatography (LC-MS/MS) is a powerful technique for the charac-terisation of proteomes. However, the diverse software platforms available for processing the raw proteomics data, each produce…
Observational health data can be leveraged to measure the real-world use and potential benefits or risks of existing medical interventions. However, lack of programming proficiency and advanced knowledge of causal inference methods excludes…
Species distribution models (SDMs) are one of the most common statistical methods to assess species occupancy and geographic distribution patterns. With the increasing complexity of ecological data, many methodological approaches have been…
Live time-lapse microscopy is essential for a wide range of biological applications. Software-based automation is the gold standard for the operation of hardware accessories necessary for image acquisition. Given that current software…
Structured Adaptive Mesh Refinement (Structured AMR) enables simulations to adapt the domain resolution to save computation and storage, and has become one of the dominant data representations used by scientific simulations; however,…
The micro-randomized trial (MRT) is a new experimental design which allows for the investigation of the proximal effects of a "just-in-time" treatment, often provided via a mobile device as part of a mobile health intervention. As with a…
When performing an aggregate data meta-analysis of a continuous outcome, researchers often come across primary studies that report the sample median of the outcome. However, standard meta-analytic methods typically cannot be directly…
Progress in hardware, algorithms, and force fields are pushing the scope of molecular dynamics (MD) simulations towards the length- and time scales of complex biochemical processes. This creates a need for developing advanced analysis…
Matrix visualizations are a useful tool to provide a general overview of a graph's structure. For multivariate graphs, a remaining challenge is to cope with the attributes that are associated with nodes and edges. Addressing this challenge,…