Related papers: BPEC: An R Package for Bayesian Phylogeographic an…

Modern phylogenetics research is often performed within a Bayesian framework, using sampling algorithms such as Markov chain Monte Carlo (MCMC) to approximate the posterior distribution. These algorithms require careful evaluation of the…

Clusters of genes that have evolved by repeated segmental duplication present difficult challenges throughout genomic analysis, from sequence assembly to functional analysis. Improved understanding of these clusters is of utmost importance,…

We introduce phylodyn, an R package for phylodynamic analysis based on gene genealogies. The package main functionality is Bayesian nonparametric estimation of effective population size fluctuations over time. Our implementation includes…

The level set tree approach of Hartigan (1975) provides a probabilistically based and highly interpretable encoding of the clustering behavior of a dataset. By representing the hierarchy of data modes as a dendrogram of the level sets of a…

The HCV package implements the hierarchical clustering for spatial data. It requires clustering results not only homogeneous in non-geographical features among samples but also geographically close to each other within a cluster. We…

Nested data structures arise when observations are grouped into distinct units, such as patients within hospitals or students within schools. Accounting for this hierarchical organization is essential for valid inference, as ignoring it can…

Spatial ecological networks are widely used to model interactions between georeferenced biological entities (e.g., populations or communities). The analysis of such data often leads to a two-step approach where groups containing similar…

A Chain Event Graph (CEG) is a graphial model which designed to embody conditional independencies in problems whose state spaces are highly asymmetric and do not admit a natural product structure. In this paer we present a probability…

Summary: Both theory and empirical evidence indicate that phylogenies (trees) of different genes (loci) do not display precisely matched topologies. This phylogenetic incongruence is attributed to the reticulated evolutionary history of…

There are many different ways in which change point analysis can be performed, from purely parametric methods to those that are distribution free. The ecp package is designed to perform multiple change point analysis while making as few…

This letter introduced a new R package 'coexist' which can perform species coexistence simulation and analysis. The package was initially developed for understanding the role of different combinations of varying species growth rates,…

We present an approach to model-based hierarchical clustering by formulating an objective function based on a Bayesian analysis. This model organizes the data into a cluster hierarchy while specifying a complex feature-set partitioning that…

Image clustering aims to partition unlabeled image datasets into distinct groups. A core aspect of this task is constructing and leveraging prior knowledge to guide the clustering process. Recent approaches introduce semantic descriptions…

Clustering of proteins is of interest in cancer cell biology. This article proposes a hierarchical Bayesian model for protein (variable) clustering hinging on correlation structure. Starting from a multivariate normal likelihood, we enforce…

The R package pdfCluster performs cluster analysis based on a nonparametric estimate of the density of the observed variables. After summarizing the main aspects of the methodology, we describe the features and the usage of the package, and…

Describing the complex dependence structure of extreme phenomena is particularly challenging. To tackle this issue we develop a novel statistical algorithm that describes extremal dependence taking advantage of the inherent hierarchical…

The moveEZ (pronounced move easy) R package provides tools for constructing animated PCA biplots that reveal how multivariate structure evolves across the ordered levels of a categorical variable. Built as an extension to the biplotEZ…

The paper presents a novel approach for unsupervised techniques in the field of clustering. A new method is proposed to enhance existing literature models using the proper Bayesian bootstrap to improve results in terms of robustness and…

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…

Super-resolution imaging techniques have largely improved our capabilities to visualize nanometric structures in biological systems. Their application further enables one to potentially quantitate relevant parameters to determine the…