Related papers: gggenomes: effective and versatile visualizations …
Genomic data visualization is essential for interpretation and hypothesis generation as well as a valuable aid in communicating discoveries. Visual tools bridge the gap between algorithmic approaches and the cognitive skills of…
GeneVis is a web-based tool to visualize complementary data sets of different disciplines within the field of genetics. It overlays gene-cluster information, gene-interaction data and gene-disease association data by means of web-based…
Motivation: The three-dimensional (3D) organization of the genome plays a critical role in regulating gene expression and maintaining cellular homeostasis. Disruptions in this spatial organization can result in abnormal chromatin…
Data visualization is a fundamental tool in genomics research, enabling the exploration, interpretation, and communication of complex genomic features. While machine learning models show promise for transforming data into insightful…
Analysis of genomics data is central to nearly all areas of modern biology. Despite significant progress in artificial intelligence (AI) and computational methods, these technologies require significant human oversight to generate novel and…
It has been shown that genome spatial structures largely affect both genome activity and DNA function. Knowing this, many researchers are currently attempting to accurately model genome structures. Despite these increased efforts there…
This paper reviews strategies for solving problems encountered when analyzing large genomic data sets and describes the implementation of those strategies in R by packages from the Bioconductor project. We treat the scalable processing,…
Data visualisation is a key tool in data mining for understanding big datasets. Many visualisation methods have been proposed, including the well-regarded state-of-the-art method t-Distributed Stochastic Neighbour Embedding. However, the…
Graphical models are a powerful tool in modelling and analysing complex biological associations in high-dimensional data. The R-package netgwas implements the recent methodological development on copula graphical models to (i) construct…
The recent advances in sequencing technologies enables the assembly of individual genomes to the reference quality. How to integrate multiple genomes from the same species and to make the integrated representation accessible to biologists…
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…
The immense increase in the generation of genomic scale data poses an unmet analytical challenge, due to a lack of established methodology with the required flexibility and power. We propose a first principled approach to statistical…
Circular genome visualizations are essential for exploring structural variants and gene regulation. However, existing tools often require complex scripting and manual configuration, making the process time-consuming, error-prone, and…
Background: Cancers are highly heterogeneous with different subtypes. These subtypes often possess different genetic variants, present different pathological phenotypes, and most importantly, show various clinical outcomes such as varied…
The R package (R Core Team (2016)) genMOSS is specifically designed for the Bayesian analysis of genome-wide association study data. The package implements the mode oriented stochastic search (MOSS) procedure as well as a simple moving…
The Genomic Foundation Model (GFM) paradigm is expected to facilitate the extraction of generalizable representations from massive genomic data, thereby enabling their application across a spectrum of downstream applications. Despite…
Several graph visualization tools exist. However, they are not able to handle large graphs, and/or they do not allow interaction. We are interested on large graphs, with hundreds of thousands of nodes. Such graphs bring two challenges: the…
Summary: With the rapid development of long-read sequencing technologies, the era of individual complete genomes is approaching. We have developed wgatools, a cross-platform, ultrafast toolkit that supports a range of whole genome alignment…
The human genome is incredibly information-rich, consisting of approximately 25,000 protein-coding genes spread out over 3.2 billion nucleotide base pairs contained within 24 unique chromosomes. The genome is important in maintaining…
Modern DNA sequencing technologies enable geneticists to rapidly identify genetic variation among many human genomes. However, isolating the minority of variants underlying disease remains an important, yet formidable challenge for medical…