scanpy-cli

A command-line interface for Scanpy, a Python library for analyzing single-cell gene expression data.

Installation

pip install scanpy-cli

Usage

The scanpy-cli tool provides three main command groups for single-cell data analysis:

Preprocessing (pp)

Commands for preprocessing single-cell data:

• filter_cells: Filter cells based on counts or genes expressed
• filter_genes: Filter genes based on counts or cells expressing them
• regress_out: Regress out unwanted sources of variation
• neighbors: Compute neighborhood graph
• pca: Run principal component analysis
• combat: Batch effect correction using ComBat
• harmony: Batch effect correction using Harmony
• scrublet: Detect doublets in single-cell RNA-seq data
• highly_variable_genes: Identify highly variable genes

Tools (tl)

Commands for analysis tools:

• umap: Run UMAP dimensionality reduction
• leiden: Run Leiden clustering
• paga: Run PAGA for trajectory inference
• rank_genes_groups: Find marker genes for clusters

Plotting (pl)

Commands for visualization:

• umap: Plot UMAP embeddings

Development

Running Tests

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
pytest

Getting Help

For help on any command, use the --help flag:

scanpy-cli --help
scanpy-cli pp --help
scanpy-cli tl umap --help