Publications
Explore 359 academic publications
Maftools: efficient and comprehensive analysis of somatic variants in cancer
Numerous large-scale genomic studies of matched tumor-normal samples have established the somatic landscapes of most cancer types. However, the downstream analysis of data from ...
How to perform a meta-analysis with R: a practical tutorial
Objective Meta-analysis is of fundamental importance to obtain an unbiased assessment of the available evidence. In general, the use of meta-analysis has been increasing over th...
GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database
Abstract Summary The Genome Taxonomy Database Toolkit (GTDB-Tk) provides objective taxonomic assignments for bacterial and archaeal genomes based on the GTDB. GTDB-Tk is computa...
JAGS: A program for analysis of Bayesian graphical models using Gibbs sampling
JAGS is a program for Bayesian Graphical modelling which aims for compatibility with Classic BUGS. The program could eventually be developed as an R package. This article explai...
Progress, Challenges, and Opportunities in Two-Dimensional Materials Beyond Graphene
Graphene's success has shown that it is possible to create stable, single and few-atom-thick layers of van der Waals materials, and also that these materials can exhibit fascina...
MCMC Methods for Multi-Response Generalized Linear Mixed Models: The<b>MCMCglmm</b><i>R</i>Package
Generalized linear mixed models provide a flexible framework for modeling a range of data, although with non-Gaussian response variables the likelihood cannot be obtained in clo...
Ultrafast Approximation for Phylogenetic Bootstrap
Nonparametric bootstrap has been a widely used tool in phylogenetic analysis to assess the clade support of phylogenetic trees. However, with the rapidly growing amount of data,...
Evaluation: from precision, recall and F-measure to ROC, informedness, markedness and correlation
Commonly used evaluation measures including Recall, Precision, F-Measure and Rand Accuracy are biased and should not be used without clear understanding of the biases, and corre...
<i>Mercury 4.0</i>: from visualization to analysis, design and prediction
The program Mercury , developed at the Cambridge Crystallographic Data Centre, was originally designed primarily as a crystal structure visualization tool. Over the years the fi...