sage_broccoliqn

Welcome to the documentation for sage_broccoliqn,
a Python package designed to ensure seamless interoperability between
AnnData (.h5ad) objects and downstream Seurat / SeuratDisk workflows in R.

Features

• Sanitizes and normalizes obs / var metadata
• Converts problematic pandas dtypes (boolean, Int64, categorical)
• Fixes HDF5 structures that cause SeuratDisk conversion errors
• Removes empty metadata columns
• Sanitizes column names to avoid HDF5 path issues
• Optional removal of heavy layers (e.g., counts_mouse)
• Writes .h5ad files compatible with SeuratDisk::Convert()

Quick Start

pip install sage_broccoliqn

Please see the Usage Guide for an example at https://github.com/denvercal1234GitHub/sage_broccoliqn

More utilities (including advanced visualisation) will be provided soon. Cheers!