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Visualization of multidimensional, categorical data is a common challenge across scientific areas and, in particular, the life sciences. The goal is to create a comprehensive overview of the underlying data which allows to assess multiple…
Meta-analysis methods are used to combine evidence from multiple studies. Meta-regression as well as model-based meta-analysis are extensions of standard pairwise meta-analysis in which information about study-level covariates and…
Clustering consists of grouping together samples giving their similar properties. The problem of modeling simultaneously groups of samples and features is known as Co-Clustering. This paper introduces ROCCO - a Robust Continuous…
SimOmics is an R package designed to generate realistic, multivariate, and multi-omics synthetic datasets. It is intended for use in benchmarking, method development, and reproducibility in bioinformatics, particularly in the context of…
The concept of "tidy data" offers a powerful framework for structuring data to ease manipulation, modeling and visualization. However, most R functions, both those built-in and those found in third-party packages, produce output that is not…
In this paper, we describe an R package named coxphMIC, which implements the sparse estimation method for Cox proportional hazards models via approximated information criterion (Su et al., 2016 Biometrics). The developed methodology is…
Compiler auto-tuning faces a dichotomy between traditional black-box search methods, which lack semantic guidance, and recent Large Language Model (LLM) approaches, which often suffer from superficial pattern matching and causal opacity. In…
Helix is an open-source, extensible, Python-based software framework to facilitate reproducible and interpretable machine learning workflows for tabular data. It addresses the growing need for transparent experimental data analytics…
This article presents a free and open source toolkit that supports the semi-automated checking of research outputs (SACRO) for privacy disclosure within secure data environments. SACRO is a framework that applies best-practice…
The R package rcosmo was developed for handling and analysing Hierarchical Equal Area isoLatitude Pixelation(HEALPix) and Cosmic Microwave Background(CMB) radiation data. It has more than 100 functions. rcosmo was initially developed for…
The ZX-calculus is a graphical language for reasoning about ZX-diagrams, a type of tensor networks that can represent arbitrary linear maps between qubits. Using the ZX-calculus, we can intuitively reason about quantum theory, and optimise…
Network analyses, such as of gene co-expression networks, metabolic networks and ecological networks have become a central approach for the systems-level study of biological data. Several software packages exist for generating and analyzing…
Spatio-temporal models for count data are required in a wide range of scientific fields and they have become particularly crucial nowadays because of their ability to analyse COVID-19-related data. Models for count data are needed when the…
ConsumerCheck is an open source data analysis software tailored for analysis of sensory and consumer data. Since some of the implemented methods are generic, such as PCA, PLSR and PCR, other data from other domains may also be analysed with…
With the advent of high-throughput sequencing (HTS) in molecular biology and medicine, the need for scalable statistical solutions for modeling complex biological systems has become of critical importance. The increasing number of platforms…
The aim of this article is to introduce a reporting framework for reproducible, interactive research applied to Big Clinical Data, based on open source technologies. The framework is constituted by the following three axes: (i) data, (ii)…
The integration of high-dimensional genomic data and clinical data into time-to-event prediction models has gained significant attention due to the growing availability of these datasets. Traditionally, a Cox regression model is employed,…
Summary: Ancestral recombination graphs (ARGs) are a complete representation of the genetic relationships between recombining lineages and are of central importance in population genetics. Recent breakthroughs in simulation and inference…
Optimizing quantum circuits is a key challenge for quantum computing. The PyZX compiler broke new ground by optimizing circuits via the ZX calculus, a powerful graphical alternative to the quantum circuit model. Still, it carries no…
RKappa is a framework for the development, simulation and analysis of rule-base models within the mature statistically empowered R environment. It is designed for model editing, parameter identification, simulation, sensitivity analysis and…