Installation

Requirements

• Python ≥ 3.9
• pip

Install from source

git clone https://github.com/IsratIJK/Upgraded-soupX.git
cd Upgraded-soupX
pip install -e .

Optional extras

Downstream analysis

Enables PCA, UMAP, tSNE, Leiden clustering, and differential expression:

pip install -e ".[downstream]"

Installs: scikit-learn>=1.0, umap-learn>=0.5, leidenalg>=0.9, python-igraph>=0.10

HDF5 support

For loading CellRanger HDF5 files (*.h5):

pip install h5py

AnnData interoperability

For SoupChannel.to_anndata() / SoupChannel.from_anndata():

pip install anndata

Development

pip install -e ".[dev]"

Installs pytest and pytest-cov.

Verify the installation

import SoupX
print(SoupX.__version__)
# 1.7.0

Environment variables

Copy .env.example to .env and fill in values needed for dataset downloads from S3:

cp .env.example .env

See the Datasets page for details.