Software

OMICS data analysis

  • ChIPseeker: ChIP peak Annotation, Comparison, and Visualization
  • GeoTcgaData: Processing various types of data on GEO and TCGA

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
  • gson: Base Class and Methods for ‘gson’ Format
  • GOSemSim: GO-terms Semantic Similarity Measures
  • meshes: MeSH Enrichment and Semantic analyses
  • ReactomePA: Reactome Pathway Analysis

Microbiome

  • MicrobiotaProcess: Analysis, visualization and biomarker discovery of microbiome
  • MMINP: Microbe-Metabolite INteractions-based metabolic profiles Predictor

Tree Data integration and visualization

  • ggmsa: Plot mutiple sequence alignment using ‘ggplot2’
  • ggtree: Visualization of tree and annotation data
  • ggtreeExtra: Phylogenetic tree data annotation
  • seqmagick: Sequence Manipulation Utilities
  • shinyTempSignal: Explore Temporal Signal of Molecular Phylogenies
  • 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
  • emojifont: Emoji and Font Awesome in Graphics
  • ggbreak: An implementation of scale functions for setting axis breaks of a ‘gg’ plot.
  • ggimage: Use Image in ‘ggplot2’
  • ggplotify: Convert Plot to ‘grob’ or ‘ggplot’ Object
  • ggstar: Multiple Geometric Shape Point Layer for ‘ggplot2’
  • meme: Create Meme
  • plotbb: Grammar of Graphics for base plot