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@YuLab-SMU Bioinformatics Group @ SMU

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    147 repositories

    • Rho

      Public
      🔬 Discover questions in the data; test explanations against the results.
      agentsscientific-research
      agentsscientific-research
      TypeScript
      •
      GNU Affero General Public License v3.0
      •9•35•16•2•Updated Nov 4, 2026Nov 4, 2026

    • Rho-plugins

      Public
      Official scientific plugins and native runtime implementations for Rho
      TypeScript
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Nov 4, 2026Nov 4, 2026

    • aisdk.acp

      Public
      Agent Client Protocol (ACP) client for driving coding agents (dsh, Claude Code, Codex) from R
      R
      •
      Other
      •0•1•0•0•Updated Nov 4, 2026Nov 4, 2026

    • aisdk.mcp

      Public
      Model Context Protocol (MCP) Client and Server for 'aisdk'
      R
      •
      Other
      •0•0•0•0•Updated Nov 4, 2026Nov 4, 2026

    • ygc-blog

      Public
      Guangchuang Yu's Blog
      TypeScript
      •
      MIT License
      •0•0•0•0•Updated Nov 3, 2026Nov 3, 2026

    • Rho-paper

      Public
      Research proposal and paper for Rho: purpose-driven, human-Agent shared analysis workspaces
      TeX
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Nov 3, 2026Nov 3, 2026

    • clusterProfiler

      Public
      :bar_chart: A universal enrichment tool for interpreting omics data
      visualizationgorstats
      visualizationgorstatskeggenrichment-analysisgsea
      R
      •268•1.2k•217•0•Updated Nov 3, 2026Nov 3, 2026

    • yulab-smu.github.io

      Public
      :house: Homepage for YuLab-SMU
      SCSS
      •6•14•0•0•Updated Nov 3, 2026Nov 3, 2026

    • ssMOOD

      Public
      ssMOOD: Major Depression Omics Online Database integrating human & mouse single-cell and spatial transcriptomics data, featuring interactive analysis powered by…
      Vue
      •
      GNU Affero General Public License v3.0
      •3•4•0•0•Updated Nov 3, 2026Nov 3, 2026

    • ChIPseeker

      Public
      :dart: ChIP peak Annotation, Comparison and Visualization
      visualizationannotationcomparison
      visualizationannotationcomparisonepigeneticschip-seqatac-seqepigenomics
      R
      •77•259•103•0•Updated Nov 3, 2026Nov 3, 2026

    • icare

      Public
      Intelligent ClinlAbomics Research Expedition
      R
      •2•2•0•1•Updated Nov 2, 2026Nov 2, 2026

    • Rho-core

      Public
      Generic Rho Host, operation journal, public protocol and SDK
      Rust
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Nov 2, 2026Nov 2, 2026

    • aplot

      Public
      Decorate a plot with associated information
      R
      •17•131•5•0•Updated Nov 1, 2026Nov 1, 2026

    • MicrobiomeProfiler

      Public
      :microbe: A shiny package for microbiome functional enrichment analysis
      R
      •9•42•1•0•Updated Nov 1, 2026Nov 1, 2026

    • treedata-book-2ed

      Public
      :book: Data Integration, Manipulation and Visualization of Phylogenetic Trees
      HTML
      •1•0•0•0•Updated Nov 1, 2026Nov 1, 2026

    • ggmsa

      Public
      :traffic_light: Visualizing publication-quality multiple sequence alignment using ggplot2
      R
      •30•220•45•0•Updated Oct 31, 2026Oct 31, 2026

    • scholar

      Public
      Analyse citation data from Google Scholar
      R
      •
      Other
      •81•54•0•0•Updated Oct 29, 2026Oct 29, 2026

    • ggtree

      Public
      :christmas_tree:Visualization and annotation of phylogenetic trees
      visualizationggplot2r
      visualizationggplot2rannotationsphylogenetic-trees
      R
      •183•935•172•0•Updated Oct 29, 2026Oct 29, 2026

    • enrichit

      Public
      C++ Implementations of Functional Enrichment Analysis
      R
      •5•4•1•0•Updated Oct 28, 2026Oct 28, 2026

    • .github

      Public
      0•0•0•0•Updated Oct 27, 2026Oct 27, 2026

    • biomedical-knowledge-mining-book

      Public
      :book: Biomedical knowledge mining using GOSemSim and clusterProfiler
      gene-ontologysemantic-similaritydisease-ontology
      gene-ontologysemantic-similaritydisease-ontologymedical-subject-headingsenrichment-analysisgosemsimclusterprofiler
      R
      •
      Other
      •30•96•1•0•Updated Oct 27, 2026Oct 27, 2026

    • treelayout

      Public
      Tree layout algorithms: compute node coordinates for phylogenetic trees without a plotting dependency
      R
      •0•1•0•0•Updated Oct 27, 2026Oct 27, 2026

    • ggcircos

      Public
      R
      •
      GNU General Public License v3.0
      •1•7•1•0•Updated Oct 26, 2026Oct 26, 2026

    • DOSE

      Public
      :mask: Disease Ontology Semantic and Enrichment analysis
      semantic-similaritydisease-ontologyenrichment-analysis
      semantic-similaritydisease-ontologyenrichment-analysis
      R
      •34•125•0•0•Updated Oct 25, 2026Oct 25, 2026

    • sclet

      Public
      A State-Aware Single-Cell and Spatial Transcriptomics Toolkit for SingleCellExperiment
      R
      •8•24•0•0•Updated Oct 24, 2026Oct 24, 2026

    • gpsadb

      Public
      R
      •
      Other
      •0•1•0•0•Updated Oct 23, 2026Oct 23, 2026

    • excercise

      Public
      HTML
      •1•0•0•0•Updated Oct 21, 2026Oct 21, 2026

    • plotbb

      Public
      :paintbrush: Grammar of Graphics on ‘base’ Graphics
      R
      •7•52•0•0•Updated Oct 18, 2026Oct 18, 2026

    • ggimage

      Public
      :art: Use Images in ggplot2
      visualizationimageggplot2
      visualizationimageggplot2r
      R
      •36•179•0•0•Updated Oct 16, 2026Oct 16, 2026

    • TCMDATA

      Public
      Traditional Chinese Medicine Data Analysis and Visualization
      R
      •3•20•0•0•Updated Oct 15, 2026Oct 15, 2026
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