Installation
System Requirements
Python 3.10 or higher
64-bit operating system (Linux, macOS, or Windows)
Minimum 8GB RAM (16GB or more recommended)
Basic Installation
Install the latest version from Source:
# Create a new conda environment
conda create -n scExtract python=3.10
conda activate scExtract
# Install scExtract
git clone https://github.com/yxwucq/scExtract
cd scExtract
pip install -e .
Dependencies
Core Dependencies
scExtract depends on the following Python packages:
Package |
Version |
Description |
|---|---|---|
python |
>=3.10 <3.13 |
Programming language |
anndata |
>=0.10.7 |
Data structure for single-cell data |
scanpy |
>=1.10.1 |
Single-cell analysis tools |
harmonypy |
>=0.0.9 |
Batch effect correction |
leidenalg |
>=0.10.2 |
Community detection |
louvain |
>=0.8.2 |
Clustering algorithm |
mygene |
>=3.2.2 |
Gene annotation |
oaklib |
>=0.6.3 |
Ontology analysis |
openai |
>=1.17.0 |
OpenAI API integration |
pypdf |
>=4.2.0 |
PDF processing |
singlecellexperiment |
>=0.4.4 |
Single cell data structure |
termcolor |
>=2.4.0 |
Terminal color output |
tqdm |
>=4.66.2 |
Progress bars |
Optional Dependencies
If you want to use the following features, you will need to install additional packages:
scanorama_prior and cellhint_prior can be installed with git and pip from the following repositories:
git clone https://github.com/yxwucq/scanorama_prior
git clone https://github.com/yxwucq/cellhint_prior
Package |
Version |
Purpose |
|---|---|---|
anthropic |
>=0.25.1 |
Anthropic API integration |
cellhint_prior |
Cell type harmonization |
|
scanorama_prior |
Batch effect correction |
|
cellhint |
>=1.0.0 |
Cell type harmonization |
singler |
>=0.4.1 |
Cell type annotation |
scanorama |
Batch effect correction |
|
cupy |
GPU acceleration |