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