BMBL Data Analysis Notebooks

Important Note: This repository is still under development and the information contained within it may change. If you have any feedback or suggestions, feel free to open an issue or reach out to us.

Browse the tutorial site: osu-bmbl.github.io/BMBL-analysis-notebooks

Purpose

This repository contains a collection of bioinformatics data analysis notebooks focused on providing examples of current best practices in single-cell analysis. The notebooks include both data and code.

Who this repository is for

This repository is intended for anyone who wants to:

1. Apply current best practices in single-cell analysis using real data.
2. Generate comprehensive reports to share with biological collaborators.
3. Find code snippets to quickly produce results and figures.

Who this repository is NOT for

This repository is NOT an introduction to data analysis. There are many available courses and resources, such as Bioinformatics Training at the Harvard Chan Bioinformatics Core and Single-cell best practices from Theis lab, that provide such introductions. The focus of this repository is on the practical aspects of analysis and assumes that users already have a basic understanding of:

1. Programming in R, Python, and Unix.
2. R markdown.
3. Assays such as RNA-seq, single-cell RNA-seq, and Spatial transcriptomics.

Table of Contents

Bioinformatics pipelines based on data type

• Single-cell RNA-seq:

  1. scRNAseq general workflow
  2. scRNAseq 10x Flex preprocessing
  3. scRNAseq trajectory_Slingshot
  4. scRNAseq CellCellCommunication
  5. scRNAseq HPV branch
  6. scRNAseq_Seurat_to_Scanpy
  7. scRNAseq stomach branch
  8. scRNAseq_ShinyCell_portal
  9. scRNAseq large dataset analysis
  10. scRNAseq_module_enrichent
  11. scRNAseq_iPSC_branch
  12. scRNAseq_immune_branch
  13. scRNAseq_inferCNV
  14. scRNAseq_label_transfer

• Single-cell ATAC-seq:

  1. scATACseq_general_workflow R
  2. scATACseq ArchR branch
  3. scATACseq Cicero branch
  4. scATACseq cisTopic branch
  5. scATACseq CellOracle workflow
  6. scATACseq ChromVAR TF motif activity
  7. scATACseq Gene activity score

• Single-cell Multi-omics:

  1. scMultiome AD branch

• Single-cell TCR-seq:

  1. scTCRseq_analysis

• RNA-seq:

  1. RNAseq general workflow nf-core

• ATAC-seq:

  1. ATACseq general workflow nf-core
  2. ATACseq_general_workflow

• Chip-seq:

  1. Chipseq general workflow
  2. Chipseq general workflow v2
  3. ChipSeq HOMER motif analysis

• Spatial Transcriptomics(ST):

  1. ST general workflow
  2. ST BayesSpace branch
  3. ST giotto branch
  4. ST spotlight branch
  5. Spatial Cellular neighborhood

• Bisulfite sequencing (BS-seq):

  1. Bismark aligner

• Whole Genome Sequencing (WGS):

  1. Low-pass WGS karyotyping workflow

• Gene Regulatory Networks (GRN):

  1. CellOracle workflow

• General downstream analysis:

  1. Enrichment Analysis Using clusterProfiler

Data Utilities

1. Download GEO supplementary files
2. Convert data to H5AD format
3. GEO data submission guide
4. Download SRA data with SRA Toolkit

Artificial Intelligence

• ChatGPT prompts
  1. ChatGPT_prompts

Other Tutorials

• Server
  1. Introduction OSC
• Figure/Plot scripts
  1. Figure codes

Contributing template

• Template Readme for all new contributions: README_template.md

Reproducible Environments (Docker & Binder)

Quick Start with Docker

Run workflows in isolated, reproducible containers:

# Start scRNA-seq workflow
docker-compose up scrnaseq

# Access RStudio at http://localhost:8788
# Username: rstudio, Password: bmbl2024

Available containers:

• scrnaseq - Single-cell RNA-seq analysis
• trajectory - Pseudotime and trajectory analysis
• scatacseq - Single-cell ATAC-seq
• rnaseq - Bulk RNA-seq
• spatial - Spatial transcriptomics

See docker/README.md for detailed instructions.

Run in the Cloud (No Installation)

Click to launch RStudio in your browser - no setup required!

For Manuscripts

For publication-ready reproducibility:

• Use environment.lock.yml for exact package versions
• Docker containers ensure identical environments
• See renv/README.md for R package locking

Questions?

If you have any questions or encounter any problems, please don't hesitate to reach out by creating an issue in this repository or contacting Shaopeng Gu at shaopeng.gu@osumc.edu.

Acknowledgements

Maintainer: Shaopeng Gu

Contributors:

• Shaopeng Gu
• Cankun Wang
• Yuzhou Chang
• Qi Guo
• Hao Cheng
• Yingjie Li
• Hu Cheng
• Weidong Wu
• Mirage Modi
• Shaohong Feng
• Ahmed Ghobashi
• Megan McNutt
• Kevin Wang
• Grace Xu

---

If you use these workflows in your research, please acknowledge: "Analysis workflows were supported by the BMBL lab and CATION (Center for AI and Translational Informatics in Oncology) at The Ohio State University Comprehensive Cancer Center."