🧬 BULLKpy 🧬

BULLKpy is a Python framework for comprehensive bulk OMICs data analysis,
with a strong focus on biomedical and cancer research.

It provides a unified, AnnData-inspired workflow to perform:

• Quality control and preprocessing

• Dimensionality reduction and clustering

• Differential expression analysis

• Pathway and gene set enrichment

• Metaprograms and tumor heterogeneity analysis

• Survival analysis and clinical associations

• Publication-ready visualization

BULLKpy on GitHub
BULLKpy on Pypi

BULLKpy is based on AnnData structures and is designed to integrate seamlessly with the scverse ecosystem, and to help standardize and democratize bulk OMICs analysis in Python.

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🚀 Installation

Clone the repository:

git clone https://github.com/malumbres/BULLKpy.git
cd BULLKpy

Install from Pypi:
(https://pypi.org/project/bullkpy/)

pip install bullkpy

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🚀 Getting started

📘 Table of contents

Contents

• Installation
• API reference
  • bullkpy
  • Input Output
  • Pre-processing
  • Tools
  • Plotting

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🚀 Tutorials

Step-by-step tutorials

Tutorial

• Notebooks
  • BULLKpy - TCGA RNAseq data
  • 1. Imports and settings
  • 2. Load data into AnnData and BULLKpy object
  • 3. Quality Control and preprocessing
  • 4. PCA and bidimensional representation
  • 5. Clustering and define groups
  • 6. Genes and Gene Signatures
  • 7. Data Exploration
  • 8. Correlations & Associations
  • 9. Markers and Differential expression
  • 10. Pathway and Gene Set Enrichment Analysis
  • 11. Metaprograms and Tumor Heterogeneity
  • 12. General Plots
  • 13. Utilities

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📦 Project structure

bullkpy-skeleton/
├── src/                # BULLKpy Python package
│   └── bullkpy/
|       ├── io.py.      # input/output tools
│       ├── pp/         # preprocessing
│       ├── tl/         # tools (DE, clustering, GSEA, associations)
│       ├── pl/         # plotting
│       └── settings.py
│
├── notebooks/          # analysis notebooks (examples, use cases)
├── data/               # large input datasets (NOT tracked by git)
├── docs/		# Read the Docs at `https://bullkpy.readthedocs.io/en/latest/` 
├── results/            # analysis outputs (NOT tracked by git)
│
├── pyproject.toml      # package configuration
├── README.md
├── CHANGELOG.md
├── LICENSE
├── .gitignore
└── .readthedocs.yaml

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🔗 Links

BULLKpy is available on GitHub (malumbres/BULLKpy).

Issue tracker: (malumbres/BULLKpy#issues)

Malumbreslab.org: (http://malumbreslab.org/)

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📄 Citation

Please refer to:
Malumbres M. (2026) BULLKpy: An AnnData-Inspired Unified Framework for Comprehensive Bulk OMICs Analysis. BioRxiv 10.64898/2026.01.26.701768v1. doi: https://doi.org/10.64898/2026.01.26.701768.

BioRxiv: (https://www.biorxiv.org/content/10.64898/2026.01.26.701768v1