Software authored by Guangchuang Yu

R/Bioconductor packages

I have developed 10 packages on CRAN and 10 on Bioconductor. For CRAN packages, you can use install.packages() to install them directly and for Bioconductor packages, you need to follow the guide on package homepage by using biocLite() to install.

If you are interesting, please visit package homepage to learn more.

  • CRAN
    • badger: Badge for R Package
    • dlstats: Download Stats of R Packages
    • emojifont: Emoji and Font Awesome in Graphics
    • ggimage: Use Image in ‘ggplot2’
    • ggplotify: Convert Plot to ‘grob’ or ‘ggplot’ Object
    • meme: Create Meme
    • rvcheck: R/Package Version Check
    • scatterpie: Scatter Pie Plot
    • shadowtext: Shadow Text Grob and Layer
    • tidytree: A Tidy Tool for Phylogenetic Tree Data Manipulation
  • Bioconductor
    • ChIPseeker: ChIPseeker for ChIP peak Annotation, Comparison, and Visualization
    • clusterProfiler: statistical analysis and visualization of functional profiles for genes and gene clusters
    • DOSE: Disease Ontology Semantic and Enrichment analysis
    • enrichplot: Visualization of Functional Enrichment Result
    • ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
    • GOSemSim: GO-terms Semantic Similarity Measures
    • meshes: MeSH Enrichment and Semantic analyses
    • ReactomePA: Reactome Pathway Analysis
    • seqcombo: Visualization Tool for Sequence Recombination and Reassortment
    • treeio: Base Classes and Functions for Phylogenetic Tree Input and Output

JAVA

  • TIPars: Taxa Insertion by Parsimony

Contributions to open source libraries

  • basicTrendline: Add Trendline and Confidence Interval of Basic Regression Models to Plot
  • cowsay: Messages, Warnings, Strings with Ascii Animals
  • kableExtra: Construct Complex Table with ‘kable’ and Pipe Syntax
  • microbiomeViz: Visualizing Microbiome Data
  • MSnbase: Base Functions and Classes for Mass Spectrometry and Proteomics
  • scholar: Analyse Citation Data from Google Scholar

MISC