# Recent Publications

More Publications

• ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data

• ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization

• ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization

• DOSE: an R/Bioconductor package for disease ontology semantic and enrichment analysis

• Putative cobalt- and nickel-binding proteins and motifs in Streptococcus pneumoniae

• A novel andrographolide derivative AL-1 exerts its cytotoxicity on K562 cells through a ROS-dependent mechanism

• LXtoo: an integrated live Linux distribution for the bioinformatics community

• clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

• Functional similarity analysis of human virus-encoded miRNAs

• A new method for measuring functional similarity of microRNAs

# Posts

### ggtree paper published

Today ggtree received 100 stars on and I found the paper was online at the same day by the tweet:

### using meshes for MeSH Enrichment Analysis

MeSH (Medical Subject Headings) is the NLM (U.S. National Library of Medicine) controlled vocabulary used to manually index articles for MEDLINE/PubMed. MeSH is comprehensive life science vocabulary. MeSH has 19 categories and MeSH.db contains 16 of them. That is:

## leading edge and core enrichment

Leading edge analysis reports Tags to indicate the percentage of genes contributing to the enrichment score, List to indicate where in the list the enrichment score is attained and Signal for enrichment signal strength.

It would also be very interesting to get the core enriched genes that contribute to the enrichment.

Now DOSE, clusterProfiler and ReactomePA all support leading edge analysis and report core enriched genes.

### How to bug author

As an author of several Bioconductor packages. I found many questions from users are quite annoying. Some of them never use google and they are reluctant to read vignettes.

### Step 1: make sure you are using the latest release

I found many peoples are using out-of-date packages. When they got an issue of an out-dated package, they never check whether the issue still exists in latest release.

### identify method for ggtree

We are happy to announce that ggtree supports interactive tree annotation/manipulation by implementing an identify method. Users can click on a node to highlight a clade, to label or rotate it etc.

Here is an example of highlighting clades using geom_hilight with identify:

# Teaching

I am a teaching instructor for the following courses at University X: