README.md

single_cell_python_tools docs

single_cell_python_tools is a collection of Scanpy-oriented wrappers and utilities for single-cell AnnData workflows. The package is commonly imported as:

import single_cell_python_tools as sctl

The public API is organized around:

• sctl.DATASET_class: a chainable dataset workflow object.
• sctl.pp: preprocessing helpers for IO, QC, normalization, PCA, and clustering.
• sctl.pl: plotting helpers for QC, clustering, batch summaries, and row-count distributions.
• sctl.tl: general Scanpy and AnnData utilities.

Documentation Pages

• Installation: conda and editable install setup.
• Quickstart: notebook setup and common workflow patterns.
• DATASET_class: chainable high-level workflow object.
• Preprocessing IO: adata.var name cleanup and layer downcasting.
• Preprocessing QC: gene annotation, QC metrics, filtering, and gene removal.
• Preprocessing Transform Data: normalization, HVG selection, regression, scaling, and PCA.
• Preprocessing Clustering: neighbors, UMAP, Leiden, renaming, and silhouette walks.
• Plotting: current plotting helpers.
• Deprecated Plotting Helpers: legacy plotting functions preserved for compatibility.
• Scanpy Tools: marker annotation, differential expression, enrichment, and data extraction helpers.
• Ingest Verbose: modified Scanpy ingest implementation.
• Example Notebooks: PBMC3k notebook entry points.
• API Reference: full static function inventory.
• Development: repo layout and docs maintenance notes.
• Troubleshooting: common setup and runtime issues.

Source Links

Core source files live under src/single_cell_python_tools. Example notebooks live under Example_notebooks.