Single cell RNA Seq Snap workflow (ScRNASeqSnap)

This repository contains tools and workflows for analyzing single cell and single nuclei RNA (sc/snRNA) data from 10X sequencing technology.

There are a Singularity and Docker image that contain all tools, packages, and dependencies necessary to run the code and analyses modules in the sc-rna-seq-snap repository. For more information on how to run the container and package versioning, please see ./run-container/README.md.

The sc-rna-seq-snap repository is an initiative of the Bioinformatics Core at the Department of Developmental Neurobiology at the St. Jude Children's Research Hospital.

⚠️ 🚧 🚧 ⚠️ The repo is currently under development and code review process.

To reproduce the code in this repository:

This repository contains tools and pipelines for the repository noted above. There is a co

1. Clone the repository

git clone https://github.com/stjude-dnb-binfcore/sc-rna-seq-snap.git

2. Navigate to an analysis module and run the shell script:

cd /home/rstudio/sc-rna-seq-snap/analyses/<module_of_interest>

To run the code in this repository with your own data:

1. Fork the repository on your own account from the main page of the stjude-dnb-binfcore/sc-rna-seq-snap by clicking the “Fork” button

2. Change the name if you like, but probably not; click “Create fork”

3. Enjoy your new project repo!

4. Replace the project_parameters.Config.yaml with your file paths and parameters.

5. How to run a module analysis

Before running a module, you will do sync fork of your project repo at GitHub, if your branch is behind the main branch of the stjude-dnb-binfcore/sc-rna-seq-snap:main. This will update the main branch of your project repo with the new code and modules (if any). This will add code and not break any analyses already run in your project repo.

Then navigate to your ./sc-rna-seq-snap project repo and ensure you are at the main branch. If not, you will need to git checkout to the main branch.

git branch
git checkout main

Finally, git pull to get the most updated changes and code in your project repo.

git pull

6. Navigate to an analysis module and run the shell script of interest:

cd ./sc-rna-seq-snap/analyses/<module_of_interest>

Below is the main directory structure listing the analyses and data files used in this repository

├── analyses
|  ├── cellranger-analysis
|  ├── fastqc-analysis
|  └── upstream-analysis
├── figures
├── LICENSE
├── project_parameters.Config.yaml
├── README.md
└── SECURITY.md

Contact

Contributions, issues, and feature requests are welcome! Please feel free to check issues.

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These tools and pipelines have been developed by the Bioinformatic core team at the St. Jude Children's Research Hospital. These are open access materials distributed under the terms of the BSD 2-Clause License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.