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.
- 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.
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.
- Docker
TCRtoolkit-SC runs in Docker containers available here. Depending on what operating system you are running (Linux, MacOS, WSL), please refer to the Docker documentation for installation instructions.
- TCRtoolkit
git clone https://github.com/KarchinLab/TCRtoolkit-SC.git
cd TCRtoolkit-SC
TBD