https://github.com/karchinlab/tcrtoolkit-sc
A NextFlow pipeline to process, analyze, and visualize single cell TCRseq data
https://github.com/karchinlab/tcrtoolkit-sc
Last synced: 4 months ago
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A NextFlow pipeline to process, analyze, and visualize single cell TCRseq data
- Host: GitHub
- URL: https://github.com/karchinlab/tcrtoolkit-sc
- Owner: KarchinLab
- Created: 2024-05-18T15:54:16.000Z (about 2 years ago)
- Default Branch: main
- Last Pushed: 2024-05-18T16:31:25.000Z (about 2 years ago)
- Last Synced: 2025-10-18T15:48:59.148Z (8 months ago)
- Language: Nextflow
- Size: 370 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# TCRtoolkit-SC: scTCR repertoire analysis
Thanks for checking out `TCRtoolkit-SC`, a platform for single cell T Cell Repertoire analysis! `TCRtoolkit-SC` is wrapped in NextFlow, written in python, and uses Docker to manage dependencies.
We are currently working on developing a pipeline to take single cell TCRseq data and perform pseudobulk analysis similar to that of `TCRtoolkit-Bulk`.
## Requirements
1. Nextflow
Nextflow can be used on any POSIX-compatible system (Linux, OS X, WSL). It requires Bash 3.2 (or later) and Java 11 (or later, up to 18) to be installed.
```{bash}
wget -qO- https://get.nextflow.io | bash
chmod +x nextflow
```
The nextflow executable is now available to run on the command line. The executable can be moved to a directory in your $PATH variable so you can run it from any directory.
2. Docker
`TCRtoolkit-SC` runs in Docker containers available [here](https://hub.docker.com/repository/docker/domebraccia/bulktcr/general). Depending on what operating system you are running (Linux, MacOS, WSL), please refer to the [Docker documentation](https://docs.docker.com/engine/install/) for installation instructions.
3. TCRtoolkit
```{bash}
git clone https://github.com/KarchinLab/TCRtoolkit-SC.git
cd TCRtoolkit-SC
```
## Quick Start
TBD