software.md

slug	title
software	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