Slide-TCR-seq jupyter notebook

This jupyter notebook contains all of the figures from the manuscript plotted.

Quickstart

Install

• You can download Jupyter, here: https://jupyter.org/install. Instructions on running Jupyter notebooks are available here: https://jupyter-notebook-beginner-guide.readthedocs.io/en/latest/execute.html.
• Download all of the data here: https://singlecell.broadinstitute.org/single_cell/study/SCP1348/slide-tcr-seq-data.
• Install packages by running the following:

  conda create --name <env> --file requirements.txt

• Download the jupyter notebook into the same directory as the data and run each block to re-create all the figures.

Additional files

• The MiXCR txt file shows an example of the commands used for MiXCR.
• The R code shows how unsupervised clustering and RCTD were performed on the data.
• save_trac_and_trbc2_constant.py shows how the TCR constant UMIs were pulled from the Slide-seq data.