Installation¶

Requirements¶

Python 3.9 or higher
Enough memory and temporary disk for the combined single-cell dataset

The normal install includes the scientific stack, PDF sequence reports, constant-region references, Excel input support, and the k-mer/TCRpeg sequence probability backends.

Install from PyPI¶

pip install tcrsift

Install from Source¶

git clone https://github.com/pirl-unc/tcrsift.git
cd tcrsift
pip install -e .

Optional Dependencies¶

Install everything, including atlas and optional plotting/report helpers:

pip install "tcrsift[full]"

Available extras:

Extra	Adds
`atlas`	Harmony, Leiden, and graph dependencies for `tcrsift cells embed`
`plots`	UpSet plots (a built-in bar-chart fallback is used without it)
`reports`	`pdfkit` for legacy HTML-to-PDF report paths
`docs`	MkDocs and the documentation theme/plugins
`dev`	pytest, coverage, Ruff, and Pylint
`full`	`atlas`, `plots`, and `reports` together

There are no assembly, excel, or tcrpeg extras. Those capabilities and dependencies are part of the core package. Constant-region assembly uses packaged canonical references; it does not require a separate pyensembl install download.

Verify Installation¶

tcrsift --version

Or in Python:

import tcrsift
print(tcrsift.__version__)