Bioinformatics Group @ SMU

• 课题组主页：https://yulab-smu.top
• 公众号：Y叔 余光创

长期招聘博士后，欢迎咨询。

We are a bioinformatics group at the School of Basic Medical Sciences, Southern Medical University (Guangzhou, China). We develop methods and open-source software that help biologists explore, interpret and communicate their data — from functional enrichment to phylogenetic trees, from single-cell atlases to AI-native analysis in R.

Our packages are distributed mainly via Bioconductor and CRAN, and are designed to work together: the same data structures, the same grammar of graphics, the same reproducible workflow.

Statistical methods and software for interpreting omics data: functional enrichment, semantic similarity, and knowledge-based annotation.

• clusterProfiler — a universal enrichment tool for interpreting omics data
• GOSemSim — semantic similarity measures among GO terms, gene products and gene clusters
• gson — base class and methods for the gson format
• enrichit — C++ implementations of functional enrichment analysis
• enrichplot — visualization of functional enrichment results
• SVP — spatially variable profiler
• DOSE · ChIPseeker · ReactomePA · meshes · geneSetEmbedding

Grammar-of-graphics extensions for the data types biologists actually work with — plots, trees, sequences, genomes, networks, and maps.

• aplot — align and combine plots with shared axes
• ggimage — use images in ggplot2
• ggbreak — axis breaks for ggplot2
• ggmsa — publication-quality multiple sequence alignment
• plotbb — grammar of graphics on base graphics
• ggsc — visualizing single-cell and spatial transcriptomics
• ggfun · ggtangle · scatterpie

A programmable environment for handling tree-structured biological data: parsing, integrating, manipulating and visualizing phylogenetic trees together with their associated data.

• ggtree — visualization and annotation of phylogenetic trees
• treeio — base classes and functions for phylogenetic tree input and output
• tidytree — tidy manipulation of phylogenetic tree data
• ggtreeExtra — add geom layers on circular or other layout trees
• treelayout — tree layout algorithms (node coordinates), extracted from ggtree
• ggtreeDendro — drawing dendrograms with ggtree

AI-native infrastructure for scientific computing in R. This is our newest direction: making AI-assisted data analysis programmable, auditable and reproducible, rather than a chat window beside the analysis.

• aisdk — a unified runtime for model providers, tool calling, agents, skills and image generation in R
• ggai — grammar-guided AI visualization: from natural-language intent to reproducible scientific figures
• Rho — an agent-native desktop workbench for R
• sclet — state-aware toolkit for single-cell and spatial transcriptomics

• You and Your Research (EN and CN)
• Can a biologist fix a radio?—Or, what I learned while studying apoptosis
• Contributions: Tree data · Knowledge mining · Visualization · AI-native scientific computing