Meijun Chen

Southern Medical University | FIMMU · School of Basic Medical Science

The data output from microbiome research is growing at an accelerating rate, yet mining the data quickly and efficiently remains difficult. There is still a lack of an effective data structure to represent and manage data, as well as flexible and composable analysis methods. In response to these two issues, we designed and developed the MicrobiotaP...

In many aspects of life, epigenetics, or the altering of phenotype without changes in sequences, play an essential role in biological function. A vast number of epigenomic datasets are emerging as a result of the advent of next‐generation sequencing. Annotation, comparison, visualization, and interpretation of epigenomic datasets remain key aspects...

Abstract While phylogenetic trees and associated data have been getting easier to generate, it has been difficult to reuse, combine, and synthesize the information they provided, because published trees are often only available as image files and associated data are often stored in incompatible formats. To increase the reproducibility and reusabili...

The toxin-antitoxin (TA) system is a widely distributed group of genetic modules that play important roles in the life of prokaryotes, with mobile genetic elements (MGEs) contributing to the dissemination of antibiotic resistance gene (ARG). The diversity and richness of TA systems in Pseudomonas aeruginosa, as one of the bacterial species with ARG...

The data output from microbiome research is growing at an accelerating rate, yet mining the data quickly and efficiently remains difficult. There is still a lack of effective data structure to represent and manage data, as well as flexible and composable analysis methods. In response to these two issues, we designed and developed the MicrobiotaProc...

With the rapid increase of large-scale datasets, biomedical data visualization is facing challenges. The data may be large, have different orders of magnitude, contain extreme values, and the data distribution is not clear. Here we present an R package ggbreak that allows users to create broken axes using ggplot2 syntax. It can effectively use the...

Functional enrichment analysis is pivotal for interpreting high-throughput omics data in life science. It is crucial for this type of tools to use the latest annotation databases for as many organisms as possible. To meet these requirements, we present here an updated version of our popular Bioconductor package, clusterProfiler 4.0. This package ha...

We present the ggtreeExtra package for visualizing heterogeneous data with a phylogenetic tree in a circular or rectangular layout (https://www.bioconductor.org/packages/ggtreeExtra). The package supports more data types and visualization methods than other tools. It supports using the grammar of graphics syntax to present data on a tree with richl...

We present the ggtreeExtra package for visualizing heterogeneous data with a phylogenetic tree (https://www.bioocnductor.org/packages/ggtreeExtra). It supports more data types and visualization methods than other tools and has many features that are not available elsewhere. The ggtreeExtra package is a universal tool for tree data visualization. It...

We present the ggtreeExtra package for visualizing heterogeneous data with a phylogenetic tree (https://www.bioconductor.org/packages/ggtreeExtra). It supports more data types and visualization methods than other tools and has many features that are not available elsewhere. The ggtreeExtra package is a universal tool for tree data visualization. It...

Folate metabolism pathway is mainly associated with syntheses of nucleic acids and proteins as well as DNA methylation and repair. Cytoplasmic C1 tetrahydrofolate (C1-THF) synthase is a central enzyme in folate metabolism and plays an important role in C1-THF conversion. The full-length sequence of silkworm (Bombyx mori) cytoplasmic C1-THF synthase...