We are a specialized computational biology team at Central South University, driving innovation in bio-intelligence and cancer genomics. Our work focuses on developing computational tools and methods for cancer research, mutational signature analysis, and bioinformatics data processing.

• blit: Bioinformatics Library for Integrated Tools - Execute command line tool from R
• geokit: Tools for Accessing and Working with the Gene Expression Omnibus (GEO)
• xbio: General bioinformatics utilities
• r-gatk: R interface for GATK tools

• mire: Microbiome Integrated Reconstruction and Estimation
• gcap: Gene-level Circular Amplicon Prediction - ecDNA detection from WES data and copy number profiles

Experimental toolkit and workflows/pipelines for bioinformatics

• oxo-flow: A Rust-native bioinformatics pipeline engine
• oxo-flow-circrna: circRNA detection pipeline
• oxo-flow-venus: a clinical-grade tumor variant detection pipeline
• oxo-flow-clindet: a comprehensive clinical pipeline ported from zyllifeworld/clindet.

• sigminer: 🌲 An easy-to-use and scalable toolkit for genomic alteration signature analysis and visualization in R
• sigflow: Streamline Analysis Workflows for Mutational Signatures (Docker/Container)
• sigminer.prediction: Train and Predict Cancer Subtype with Keras Model based on Mutational Signatures
• bregr: Easy and Efficient Batch Processing of Regression Models in R
• ezcox: Easily Process a Batch of Cox Models
• SigBridgeR: Screening for phenotype-associated cells at the single-cell level
• SigBridgeRUtils: Utilities for SigBridgeR
• Bizard: A Biomedical Visualization Atlas https://openbiox.github.io/Bizard/
• metawho: 📦 An R package implementing deft approach for meta analysis
• neopeptides: Calculate and explore property indices of peptides for cancer immunotherapy study

• faers: R interface for FDA Adverse Event Reporting System (Bioconductor)
• UCSCXenaTools: 📦 An R package for accessing genomics data from UCSC Xena platform (rOpenSci, CRAN)
• UCSCXenaShiny: 📊 An R package for interactively exploring UCSC Xena
• IDConverter: Convert Identifiers in Biological Databases
• rsra: Download NCBI SRA data

• DoAbsolute: 📦 Automate Absolute Copy Number Calling using 'ABSOLUTE' package
• install_GISTIC: Install GISTIC2 by one line code; GISTIC2 docker image
• Variants2Neoantigen: A neoantigen calling pipeline begins from variants record file (MAF)
• tinyscholar: A Tiny R Package to Get and Show Google Scholar Profile
• sync-deploy: Shell toolkit for deploying script/command task on remote host
• contribution: A Tiny Contribution Table Generator Based on ggplot2

• Lab Website
• R-universe packages
• Shixiang's R-universe

• Linux for bioinformatics: The Unix Workbench | book of Bioinformatics Data Skills

• R for data science: book of R for Data Science | book of R4DS | tidyverse | easystats

• Python for data science: book of Python for Data Analysis | book of Python Data Science Handbook | Single-cell analysis in Python

• R package development: Tidy design principles | Tidyverse style guide | Yunuuuu/standalone | R Packages (2e)

  • utils: https://github.com/Yunuuuu/standalone https://github.com/WangLabCSU/rpkgkit

• Advanced: Advanced R | ggplot2: Elegant Graphics for Data Analysis | The R Manuals | Rcpp for everyone

• Web development: Shiny | Mastering Shiny | Resources for Developers, by Developers | devdocs | microsoft learn

• AI related:

  • AI coding: https://github.com/WangLabCSU/skills https://github.com/WangLabCSU/ai-rollup (team maintain) https://github.com/WangLabCSU/andrej-karpathy-skills
  • agents: https://github.com/WangLabCSU/bioinfo-daily-skill https://github.com/WangLabCSU/bioinformatics-god-skill https://github.com/WangLabCSU/zhuge-perspective-skill https://github.com/WangLabCSU/nobel-medicine-minds
  • skill collection: https://github.com/GPTomics/bioSkills https://github.com/WangLabCSU/OpenClaw-Medical-Skills https://github.com/WangLabCSU/medical-research-skills
  • tutorials: https://github.com/anthropics/courses https://labuladong.online/zh/ai-coding/ai-guide/ https://github.com/WangLabCSU/dive-into-llms https://github.com/WangLabCSU/minimind, More check https://github.com/datawhalechina
  • writing: https://github.com/Imbad0202/academic-research-skills https://github.com/aiming-lab/AutoResearchClaw/blob/main/docs/README_CN.md

• Cookbook-for-R-Chinese: 📚Cookbook for R 中文翻译 https://openbiox.github.io/Cookbook-for-R-Chinese/
• Curated-List: A Curated Reading List Maintained by Shixiang and His Team
• courses: Lecture notes and tutorials
• weekly