Welcome to the bioinformatics code repository of the Human Innate Lymphoid Cell Lab led by Jenny Mjösberg at Karolinska Institutet.

The Jenny Mjösberg group conducts translational research to characterize the role of innate lymphoid cells (ILCs) in intestinal inflammation, cancer, and asthma. We address complex immunological questions using unique tissue material from patients and employ advanced single-cell based techniques including:

• Flow cytometric analysis and sorting
• In vitro cell assays
• Single-cell RNA-sequencing (scRNA-seq)
• Single-cell ATAC-seq
• Multi-modal analysis

Our research is performed at the Center for Infectious Medicine (CIM) and the Clinical Lung and Allergy Research Unit (CLARU) at Karolinska Institutet.

🔗 Lab Website

This organization hosts bioinformatics code and computational workflows developed within the lab, primarily focused on:

• Single-cell transcriptomics analysis (scRNA-seq, scATAC-seq)
• Flow cytometry data analysis
• Integrated multi-modal data analysis

Public repository of the manuscript "Tumor-infiltrating immature innate lymphoid cells in colorectal cancer are biased towards tissue-resident NK cell/ILC1 differentiation"

Our computational pipelines primarily use:

• Languages: R, Python
• Key R packages: Seurat, SingleCellExperiment, Monocle3, WGCNA
• Python tools: scVelo, scanpy, scRNA-seq analysis tools
• Visualization: ggplot2, matplotlib, interactive 3D UMAP plots
• Version control: Git/GitHub

Each project repository contains:

• README.md - Project-specific documentation
• Setup scripts (e.g., 00_setup.R) - Environment configuration and package installation
• Numbered analysis scripts - Sequential workflow steps
• Jupyter notebooks (.ipynb) - Interactive analysis and visualization

Please refer to individual repository documentation for specific installation requirements and usage instructions.

We welcome collaboration and contributions! If you're working with our code:

1. Check project-specific CONTRIBUTING.md files for guidelines
2. Use descriptive commit messages
3. Document new functions and analysis steps
4. Include references to relevant publications or methods

Our research findings are published in peer-reviewed journals. Code in this repository supports published and ongoing research projects. Please check individual repositories for citation information.

Principal Investigator: Jenny Mjösberg
Institution: Karolinska Institutet, Department of Medicine, Huddinge
Location: Stockholm, Sweden

For scientific inquiries about the research or collaborations, please visit our lab website for contact information.

For questions about the code or bioinformatics analyses, please open an issue in the relevant repository.

Unless otherwise specified, code in this organization is available under open-source licenses. Please check individual repositories for specific licensing information.

Part of the Center for Infectious Medicine (CIM) and Clinical Lung and Allergy Research Unit (CLARU)
Karolinska Institutet, Stockholm, Sweden