Software

ChIP-seq

  • ChIPseeker: ChIP peak Annotation, Comparison, and Visualization

Infectious disease and Epidemiology

  • nCov2019: An R package for exploring COVID-19 statistics
  • seqcombo: Visualization Tool for Sequence Recombination and Reassortment

Knowledge mining

  • 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
  • GOSemSim: GO-terms Semantic Similarity Measures
  • meshes: MeSH Enrichment and Semantic analyses
  • ReactomePA: Reactome Pathway Analysis

Microbiome

Phylogeny

  • ggmsa: Plot mutiple sequence alignment using ‘ggplot2’
  • ggtree: Visualization of tree and annotation data
  • ggtreeExtra: Phylogenetic tree data annotation
  • seqmagick: Sequence Manipulation Utilities
  • tidytree: A Tidy Tool for Phylogenetic Tree Data Manipulation
  • treeio: Base Classes and Functions for Phylogenetic Tree Input and Output

Visualization

  • aplot: Decorating a plot with associated information
  • plotbb: Grammar of Graphics for base plot