Batch Effects Python Packages

batchlens-bio

Metadata-only experimental-design and batch-confounding audits for single-cell and spatial studies

sccausalvi

Perturbational analysis by causality-aware generative model for single-cell RNA-sequencing data

mnnpy

An implementation of MNN (Mutual Nearest Neighbors) correct in python.

artificial-data-generator

Synthetic biomedical data generator for reproducible benchmarking of feature selection methods in high-dimensional machine learning.

biomedical-data-generator

Synthetic biomedical data generator for reproducible benchmarking of feature selection methods in high-dimensional machine learning.

cohortlint

Pre-integration metadata diagnostics for multi-cohort omics studies — design confounding, harmonization, privacy hygiene, and multilingual reports.