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Microbiome data analysis is essential for understanding host health and disease, yet its inherent sparsity and noise pose major challenges for accurate imputation, hindering downstream tasks such as biomarker discovery. Existing imputation…
Correlation among the observations in high-dimensional regression modeling can be a major source of confounding. We present a new open-source package, plmmr, to implement penalized linear mixed models in R. This R package estimates…
Structural assessment of biomolecular complexes is vital for translating molecular models into functional insights, shaping our understanding of biology and aiding drug discovery. However, current structure-based scoring functions often…
Gaussian process (GP) models are commonly used statistical metamodels for emulating expensive computer simulators. Fitting a GP model can be numerically unstable if any pair of design points in the input space are close together. Ranjan,…
Integrating multiple observational studies for meta-analysis has sparked much interest. The presented R package WMAP (Weighted Meta-Analysis with Pseudo-Population) addresses a critical gap in the implementation of integrative weighting…
In clinical trials, identification of prognostic and predictive biomarkers is essential to precision medicine. Prognostic biomarkers can be useful for the prevention of the occurrence of the disease, and predictive biomarkers can be used to…
In a world with data that change rapidly and abruptly, it is important to detect those changes accurately. In this paper we describe an R package implementing a generalized version of an algorithm recently proposed by Hocking et al. [2020]…
Accurate diagnostic tests are essential for effective screening and treatment. However, individual biomarkers often fail to provide sufficient diagnostic accuracy, as they typically capture only one aspect of the complex disease process.…
We introduce an R package, PCMBase, to rapidly calculate the likelihood for multivariate phylogenetic comparative methods. The package is not specific to particular models but offers the user the functionality to very easily implement a…
We present vir, an R package for variational inference with shrinkage priors. Our package implements variational and stochastic variational algorithms for linear and probit regression models, the use of which is a common first step in many…
The synthpop package for R https://www.synthpop.org.uk provides tools to allow data custodians to create synthetic versions of confidential microdata that can be distributed with fewer restrictions than the original. The synthesis can be…
Gene expression profiling technologies have been used in various applications such as cancer biology. The development of gene expression profiling has expanded the scope of target discovery in transcriptomic studies, and each technology…
Recommendation systems in AI-based medical diagnostics and treatment constitute a critical component of AI in healthcare. Although some studies have explored this area and made notable progress, healthcare recommendation systems remain in…
Neural networks have excelled at regression and classification problems when the input space consists of scalar variables. As a result of this proficiency, several popular packages have been developed that allow users to easily fit these…
The gut microbiome, crucial for human health, presents challenges in analyzing its complex metaomic data due to high dimensionality and sparsity. Traditional methods struggle to capture its intricate relationships. We investigate graph…
Growing evidence from recent studies implies that microRNA or miRNA could serve as biomarkers in various complex human diseases. Since wet-lab experiments are expensive and time-consuming, computational techniques for miRNA-disease…
Analysis of the sequence-structure relationship in RNA molecules are essential to evolutionary studies but also to concrete applications such as error-correction methodologies in sequencing technologies. The prohibitive sizes of the…
Differential abundance analysis is at the core of statistical analysis of microbiome data. The compositional nature of microbiome sequencing data makes false positive control challenging. Here, we show that the compositional effects can be…
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,…
In recent years there has been widespread concern in the scientific community over a reproducibility crisis. Among the major causes that have been identified is statistical: In many scientific research the statistical analysis (including…