Repositories list

• ygc-blog

  Public
  Guangchuang Yu's Blog

  TypeScript

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 5, 2026May 5, 2026

• aisdk

  Public
  🤖 A production-grade framework for building AI-powered applications in R.

  R

  •

  Other

  •55 forks•4444 stars•11 issue•00 pull requests•Updated May 5, 2026May 5, 2026

• biomedical-knowledge-mining-book

  Public
  :book: Biomedical knowledge mining using GOSemSim and clusterProfiler

  gene-ontologysemantic-similaritydisease-ontology+ 4

  gene-ontologysemantic-similaritydisease-ontologymedical-subject-headingsenrichment-analysisgosemsimclusterprofiler

  TeX

  •3030 forks•9393 stars•2020 issues•00 pull requests•Updated May 3, 2026May 3, 2026

• treedata-book-2ed

  Public
  :book: Data Integration, Manipulation and Visualization of Phylogenetic Trees

  HTML

  •11 fork•00 stars•00 issues•00 pull requests•Updated May 3, 2026May 3, 2026

• clusterProfiler

  Public

  YuLab-SMU/clusterProfiler’s past year of commit activity
  :bar_chart: A universal enrichment tool for interpreting omics data

  visualizationgorstats+ 3

  visualizationgorstatskeggenrichment-analysisgsea

  R

  •266266 forks•1.2k1.2k stars•366366 issues•00 pull requests•Updated May 3, 2026May 3, 2026

• yulab-smu.github.io

  Public
  :house: Homepage for YuLab-SMU

  HTML

  •66 forks•1414 stars•00 issues•00 pull requests•Updated May 2, 2026May 2, 2026

• ggai

  Public
  R

  •

  Other

  •11 fork•77 stars•00 issues•00 pull requests•Updated May 1, 2026May 1, 2026

• treeio

  Public
  :seedling: Base Classes and Functions for Phylogenetic Tree Input and Output

  parserexporterphylogenetic-trees

  parserexporterphylogenetic-trees

  R

  •2525 forks•104104 stars•2727 issues•00 pull requests•Updated Apr 30, 2026Apr 30, 2026

• ggtreeExtra

  Public
  :lemon: Add Geom Layers On Circular Or Other Layout Tree Of “ggtree”

  R

  •

  GNU General Public License v3.0

  •1818 forks•9797 stars•1313 issues•00 pull requests•Updated Apr 29, 2026Apr 29, 2026

• SVP

  Public
  Spatially Variable Profiler

  R

  •

  GNU General Public License v3.0

  •00 forks•1212 stars•00 issues•00 pull requests•Updated Apr 29, 2026Apr 29, 2026

• MicrobiotaProcess

  Public
  :microbe: A comprehensive R package for deep mining microbiome

  rstatsmicrobiomemicrobiome-analysis+ 1

  rstatsmicrobiomemicrobiome-analysismicrobiome-data

  R

  •3737 forks•192192 stars•9393 issues•00 pull requests•Updated Apr 29, 2026Apr 29, 2026

• seqcombo

  Public
  Visualization tool for genetic reassortment

  R

  •77 forks•2121 stars•11 issue•00 pull requests•Updated Apr 29, 2026Apr 29, 2026

• ReactomePA

  Public
  Reactome Pathway Analysis

  enrichment-analysisreactome-pathway-analysisreactomepa

  enrichment-analysisreactome-pathway-analysisreactomepa

  R

  •1010 forks•4545 stars•1818 issues•00 pull requests•Updated Apr 29, 2026Apr 29, 2026

• MicrobiomeProfiler

  Public
  :microbe: A shiny package for microbiome functional enrichment analysis

  R

  •88 forks•4040 stars•00 issues•11 pull request•Updated Apr 29, 2026Apr 29, 2026

• ggtreeSpace

  Public
  🕸️Exploring phylomorphospace using 'ggtree'

  R

  •22 forks•55 stars•00 issues•00 pull requests•Updated Apr 29, 2026Apr 29, 2026

• meshes

  Public
  :stethoscope: MeSH Enrichment and Semantic analyses

  semantic-similaritymedical-subject-headingsenrichment-analysis

  semantic-similaritymedical-subject-headingsenrichment-analysis

  R

  •44 forks•1212 stars•22 issues•11 pull request•Updated Apr 29, 2026Apr 29, 2026

• GOSemSim

  Public
  :golf: GO-terms Semantic Similarity Measures

  bioinformaticsgene-ontologysemantic-similarity

  bioinformaticsgene-ontologysemantic-similarity

  R

  •2424 forks•7070 stars•1414 issues•00 pull requests•Updated Apr 29, 2026Apr 29, 2026

• ggtreeDendro

  Public
  Drawing 'dendrogram' using 'ggtree'

  clusteringdendrogram

  clusteringdendrogram

  R

  •33 forks•1313 stars•00 issues•00 pull requests•Updated Apr 29, 2026Apr 29, 2026

• ggsc

  Public
  🧠 Visualizing Single Cell and Spatial Transcriptomics

  R

  •1212 forks•5151 stars•00 issues•00 pull requests•Updated Apr 29, 2026Apr 29, 2026

• ggmsa

  Public
  :traffic_light: Visualizing publication-quality multiple sequence alignment using ggplot2

  R

  •2727 forks•217217 stars•5050 issues•00 pull requests•Updated Apr 29, 2026Apr 29, 2026

• epiSeeker

  Public
  epiSeeker: an R package for Annotation, Comparison and Visualization of multi-omics epigenetic data

  R

  •11 fork•00 stars•00 issues•00 pull requests•Updated Apr 29, 2026Apr 29, 2026

• enrichplot

  Public
  Visualization of Functional Enrichment Result

  visualizationpathway-analysisenrichment-analysis

  visualizationpathway-analysisenrichment-analysis

  R

  •7575 forks•258258 stars•121121 issues•00 pull requests•Updated Apr 29, 2026Apr 29, 2026

• DOSE

  Public
  :mask: Disease Ontology Semantic and Enrichment analysis

  semantic-similaritydisease-ontologyenrichment-analysis

  semantic-similaritydisease-ontologyenrichment-analysis

  R

  •3434 forks•125125 stars•2222 issues•00 pull requests•Updated Apr 29, 2026Apr 29, 2026

• ChIPseeker

  Public
  :dart: ChIP peak Annotation, Comparison and Visualization

  visualizationannotationcomparison+ 4

  visualizationannotationcomparisonepigeneticschip-seqatac-seqepigenomics

  R

  •7878 forks•254254 stars•116116 issues•11 pull request•Updated Apr 29, 2026Apr 29, 2026

• ggtree

  Public
  :christmas_tree:Visualization and annotation of phylogenetic trees

  visualizationggplot2r+ 2

  visualizationggplot2rannotationsphylogenetic-trees

  R

  •184184 forks•927927 stars•193193 issues•00 pull requests•Updated Apr 29, 2026Apr 29, 2026

• ggtangle

  Public
  Draw Network with Data

  R

  •33 forks•1010 stars•00 issues•00 pull requests•Updated Apr 24, 2026Apr 24, 2026

• sclet

  Public
  A Lightweight Toolkit for Single-Cell Data Analysis

  R

  •77 forks•99 stars•00 issues•11 pull request•Updated Apr 22, 2026Apr 22, 2026

• aisdk.bioc

  Public
  R

  •

  Other

  •11 fork•00 stars•00 issues•11 pull request•Updated Apr 16, 2026Apr 16, 2026

• bioinformatics-course

  Public
  HTML

  •00 forks•44 stars•00 issues•00 pull requests•Updated Apr 15, 2026Apr 15, 2026

• TCMDATA

  Public
  Traditional Chinese Medicine Data Analysis and Visualization

  R

  •33 forks•1414 stars•00 issues•00 pull requests•Updated Apr 12, 2026Apr 12, 2026