Related papers: wtest: an R Package for Testing Main and Interacti…
The R package micompr implements a procedure for assessing if two or more multivariate samples are drawn from the same distribution. The procedure uses principal component analysis to convert multivariate observations into a set of linearly…
We consider in this paper detection of signal regions associated with disease outcomes in whole genome association studies. Gene- or region-based methods have become increasingly popular in whole genome association analysis as a…
Rgbp is an R package that provides estimates and verifiable confidence intervals for random effects in two-level conjugate hierarchical models for overdispersed Gaussian, Poisson, and Binomial data. Rgbp models aggregate data from k…
Motivated by the important problem of detecting association between genetic markers and binary traits in genome-wide association studies, we present a novel Bayesian model that establishes a hierarchy between markers and genes by defining…
Bayesian networks (BNs) are widely used for modeling complex systems with uncertainty, yet repositories of pre-built BNs remain limited. This paper introduces bnRep, an open-source R package offering a comprehensive collection of documented…
An important problem in the field of bioinformatics is to identify interactive effects among profiled variables for outcome prediction. In this paper, a logistic regression model with pairwise interactions among a set of binary covariates…
Gene-environment and nutrition-environment studies often involve testing of high-dimensional interactions between two sets of variables, each having potentially complex nonlinear main effects on an outcome. Construction of a valid and…
The development of next generation sequencing (NGS) technology and genotype imputation methods enabled researchers to measure both common and rare variants in genome-wide association studies (GWAS). Statistical methods have been proposed to…
MicroTrace is an open-source R tool that performs SNP-based hierarchical clustering to detect potential transmission clusters from pathogen whole-genome sequencing (WGS) data. Designed for epidemiologists, microbiologists, and genomic…
The use of Bayesian adaptive designs for randomised controlled trials has been hindered by the lack of software readily available to statisticians. We have developed a new software package (Bayesian Adaptive Trials Simulator Software -…
The R package knnwtsim provides functions to implement k nearest neighbors (KNN) forecasting using a similarity metric tailored to the forecasting problem of predicting future observations of a response series where recent observations,…
Motivation: Proteomic mass spectrometry analysis is becoming routine in clinical diagnostics, for example to monitor cancer biomarkers using blood samples. However, differential proteomics and identification of peaks relevant for class…
The objective of a genome-wide association study (GWAS) is to associate subsequences of individuals' genomes to the observable characteristics called phenotypes (e.g., high blood pressure). Motivated by the GWAS problem, in this paper we…
Motivated by genetic association studies of SNPs with genotype uncertainty, we propose a generalization of the Kruskal-Wallis test that incorporates group uncertainty when comparing k samples. The extended test statistic is based on…
Under complete linkage disequilibrium (LD), robust tests often have greater power than Pearson's chi-square test and trend tests for the analysis of case-control genetic association studies. Robust statistics have been used in…
Motivation: Although principal component analysis (PCA) is widely used for the dimensional reduction of biomedical data, interpretation of PCA results remains daunting. Most existing methods attempt to explain each principal component (PC)…
Spatial transcriptomics (ST) provides crucial insights into tissue micro-environments, but is limited to its high cost and complexity. As an alternative, predicting gene expression from pathology whole slide images (WSI) is gaining…
In genetic association studies, a single marker is often associated with multiple, correlated phenotypes (e.g., obesity and cardiovascular disease, or nicotine dependence and lung cancer). A pervasive question is then whether that marker…
Crossover designs are widely applied in medicine, agriculture, and other biological sciences, yet their analysis remains challenging due to longitudinal observations within each unit and the presence of carry-over effects. Despite their…
Genome-wide association studies (GWAS) have led to the discovery of numerous single nucleotide polymorphisms (SNPs) associated with various phenotypes and complex diseases. However, the identified genetic variants do not fully explain the…