Related papers: wTO: an R package for computing weighted topologic…
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…
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…
This R package evaluates main and pair-wise interaction effect of single nucleotide polymorphisms (SNPs) via the W-test, scalable to whole genome-wide data sets. The package provides fast and accurate p-value estimation of genetic markers,…
Propensity score weighting is an important tool for comparative effectiveness research.Besides the inverse probability of treatment weights (IPW), recent development has introduced a general class of balancing weights, corresponding to…
Algorithms for detecting clusters (including overlapping clusters) in graphs have received significant attention in the research community. A closely related important aspect of the problem -- quantification of statistical significance of…
Motivation: Gene regulatory interactions are of fundamental importance to various biological functions and processes. However, only a few previous computational studies have claimed success in revealing genome-wide regulatory landscapes…
Multiplex networks describe a large number of systems ranging from social networks to the brain. These multilayer structure encode information in their structure. This information can be extracted by measuring the correlations present in…
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…
Network alignment aims to uncover topologically similar regions in the protein-protein interaction (PPI) networks of two or more species under the assumption that topologically similar regions tend to perform similar functions. Although…
The behaviour of gene regulatory networks (GRNs) is typically analysed using simulation-based statistical testing-like methods. In this paper, we demonstrate that we can replace this approach by a formal verification-like method that gives…
We review the main tools which allow for the statistical characterization of weighted networks. We then present two case studies, the airline connection network and the scientific collaboration network, which are representative of critical…
Kernel density estimation is a well known method involving a smoothing parameter (the bandwidth) that needs to be tuned by the user. Although this method has been widely used the bandwidth selection remains a challenging issue in terms of…
Motivation: We introduce TRONCO (TRanslational ONCOlogy), an open-source R package that implements the state-of-the-art algorithms for the inference of cancer progression models from (epi)genomic mutational profiles. TRONCO can be used to…
Networks are useful for representing phenomena in a broad range of domains. Although their ability to represent complexity can be a virtue, it is sometimes useful to focus on a simplified network that contains only the most important edges:…
Gene expression-based heterogeneity analysis has been extensively conducted. In recent studies, it has been shown that network-based analysis, which takes a system perspective and accommodates the interconnections among genes, can be more…
Free and open source software package ecosystems have existed for a long time and are among the most sophisticated human-made systems. One of the oldest and most popular software package ecosystems is CRAN, the repository of packages of the…
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…
Rank-Biased Overlap (RBO) is a similarity measure for indefinite rankings: it is top-weighted, and can be computed when only a prefix of the rankings is known or when they have only some items in common. It is widely used for instance to…
Modelling gene regulatory networks not only requires a thorough understanding of the biological system depicted but also the ability to accurately represent this system from a mathematical perspective. Throughout this chapter, we aim to…
In computational biology, biological entities such as genes or proteins are usually annotated with terms extracted from Gene Ontology (GO). The functional similarity among terms of an ontology is evaluated by using Semantic Similarity…