Recent Publications

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

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

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

    Details PDF Code Project

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

    Details PDF Code Project

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

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

    Details PDF

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

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

    Details PDF Code Project

  • Functional similarity analysis of human virus-encoded miRNAs

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  • A new method for measuring functional similarity of microRNAs

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OutbreakTools implements basic tools for the analysis of Disease Outbreaks.

It defines S4 class obkData to store case-base outbreak data. It also provides a function, plotggphy, to visualize such data on the phylogenetic tree.

library(OutbreakTools)
data(FluH1N1pdm2009)
attach(FluH1N1pdm2009)


x <- new("obkData", individuals = individuals, dna = FluH1N1pdm2009$dna,
         dna.individualID = samples$individualID, dna.date = samples$date,
         trees = FluH1N1pdm2009$trees)

plotggphy(x, ladderize = TRUE, branch.unit = "year",
          tip.color = "location", tip.size = 3, tip.alpha = 0.75)

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ggtree can parse many software outputs and the evolution evidences inferred by these software can be used directly for tree annotation. ggtree not only works as an infrastructure that enables evolutionary data that inferred by commonly used software packages to be used in R, but also serves as a general tree visualization and annotation tool for the R community as it supports many S3/S4 objects defined by other R packages.

phyloseq for microbiome data

phyloseq class defined in the phyloseq package was designed for microbiome data. phyloseq package implemented plot_tree function using ggplot2. Although the function was implemented by ggplot2 and we can use theme, scale_color_manual etc for customization, the most valuable part of ggplot2, adding layer, is missing. plot_tree only provides limited parameters to control the output graph and it is hard to add layer unless user has expertise in both phyloseq and ggplot2.

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

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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:

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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.

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Teaching

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