Infectious disease and Epidemiology
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- nCov2019: An R package for exploring COVID-19 statistics
- seqcombo: Visualization Tool for Sequence Recombination and Reassortment
- 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
- HDO.db: A set of annotation maps describing the entire Human Disease Ontology
- meshes: MeSH Enrichment and Semantic analyses
- ReactomePA: Reactome Pathway Analysis
- MicrobiotaProcess: Analysis, visualization and biomarker discovery of microbiome
- MMINP: Microbe-Metabolite INteractions-based metabolic profiles Predictor
- ChIPseeker: ChIP peak Annotation, Comparison, and Visualization
- GeoTcgaData: Processing various types of data on GEO and TCGA
- ggmsa: Plot mutiple sequence alignment using ‘ggplot2’
- seqmagick: Sequence Manipulation Utilities
Tree Data integration and visualization
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- ggtree: Visualization of tree and annotation data
- ggtreeDendro: Drawing ‘dendrogram’ using ‘ggtree’
- ggtreeExtra: Phylogenetic tree data annotation
- 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
- 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
- scatterpie: Creates scatterpie plots, especially useful for plotting pies on a map