A command-line interface for Scanpy, a Python library for analyzing single-cell gene expression data.
pip install scanpy-cliThe scanpy-cli tool provides three main command groups for single-cell data analysis:
Commands for preprocessing single-cell data:
filter_cells: Filter cells based on counts or genes expressedfilter_genes: Filter genes based on counts or cells expressing themregress_out: Regress out unwanted sources of variationneighbors: Compute neighborhood graphpca: Run principal component analysiscombat: Batch effect correction using ComBatharmony: Batch effect correction using Harmonyscrublet: Detect doublets in single-cell RNA-seq datahighly_variable_genes: Identify highly variable genesscanorama: Run Scanorama for batch effect correctionbbknn: Run BBKNN for batch effect correction
Commands for analysis tools:
umap: Run UMAP dimensionality reductionleiden: Run Leiden clusteringpaga: Run PAGA for trajectory inferencerank_genes_groups: Find marker genes for clusters
Commands for visualization:
umap: Plot UMAP embeddings
To run the tests, you'll need to install the package with the test dependencies:
# Install in development mode with test dependencies
pip install -e ".[testing]"
# Run the tests with pytest
pytestFor help on any command, use the --help flag:
scanpy-cli --help
scanpy-cli pp --help
scanpy-cli tl umap --help