Installation

Requirements

• Python 3.9 or higher
• numpy, pandas, scanpy, anndata (core dependencies)
• matplotlib, seaborn (visualization)

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 all optional feature bundles:

pip install "tcrsift[reports,assembly,excel]"

PDF Report Generation

For generating PDF reports:

pip install "tcrsift[reports]"

You'll also need wkhtmltopdf:

macOSUbuntu/DebianWindows

brew install wkhtmltopdf

sudo apt-get install wkhtmltopdf

Download from wkhtmltopdf.org

Ensembl Data for Constant Regions

For assembling full-length TCR sequences with constant regions:

pip install "tcrsift[assembly]"
pyensembl install --release 93 --species human

Excel Support

For SCT Excel input files:

pip install "tcrsift[excel]"

Verify Installation

tcrsift --version

Or in Python:

import tcrsift
print(tcrsift.__version__)