sjanpy

Subjacent Analysis Toolkits for Single-Cell Omics in Python

A collection of visualization and analysis utilities for single-cell RNA-seq workflows. Built on top of Scanpy and AnnData.

sjanpy follows the Scanpy subpackage convention:

• sjanpy.pl – Plotting: embeddings, dotplots, bar plots, volcano plots, Nebulosa density

• sjanpy.tl – Tools: differential expression analysis, Pearson residuals normalization

• sjanpy.pp – Preprocessing: gene filtering, stratified splitting, HVG selection

• sjanpy.ml – Machine Learning: h5ad I/O, standardization, dataset building (safetensors/pt), GPU/streaming datasets

Getting Started

• Installation
  • From source
  • Dependencies

Tutorials

• Tutorials
  • Plotting
  • Analysis
  • Preprocessing

API Reference

• API Reference
  • Plotting (sjanpy.pl)
  • Tools (sjanpy.tl)
  • Preprocessing (sjanpy.pp)
  • Machine Learning (sjanpy.ml)