tcrdist2 is a python API-enabled toolkit for analyzing T-cell receptor repertoires. Some of the functionality and code is adapted from the original tcr-dist package which was released with the publication of Dash et al. Nature (2017) doi:10.1038/nature22383. This package contains a new API for accessing the features of tcr-dist, as well as many new features that expand the T cell receptor analysis pipeline.
The original code for replicating analysis performed in the manuscript can be found here.
Documentation, installation instructions, information about dependencies, and examples can be found at tcrdist2.readthedocs.io
The development version of tcrdist2 compatible with Python 3.6 or later. It can be cloned or installed directly.
pip install git+https://github.com/kmayerb/tcrdist2.git@API2
To test out code used in the documented examples. Create a venv. Install tcrdist2 with all dependencies.
python3 -m venv ./tenv
source tenv/bin/activate
pip install git+https://github.com/kmayerb/tcrdist2.git
Quickly test installation
python -c "import tcrdist"
If you wish, use the following set of commands to install testing files and legacy blast (replace the download_from
argument to 'dropbox_osx'
or 'dropbox_linux'
based on your operating system).
python -c "import tcrdist as td; td.install_test_files.install_test_files()"
python -c "import tcrdist as td; td.setup_db.install_all_next_gen()"
python -c "import tcrdist as td; td.setup_blast.install_blast_to_externals(download_from = 'dropbox_osx')"
Pradyot Dash, Andrew J. Fiore-Gartland, Tomer Hertz, George C. Wang, Shalini Sharma, Aisha Souquette, Jeremy Chase Crawford, E. Bridie Clemens, Thi H. O. Nguyen, Katherine Kedzierska, Nicole L. La Gruta, Philip Bradley & Paul G. Thomas
Zachary Sethna, Yuval Elhanati, Curtis G Callan, Aleksandra M Walczak, Thierry Mora
(tcrdist2 incorporates OLGA for generation probability estimates)
Jeff Daily
(tcrdist2 depends on Parasail for fast sequence alignment)