Utilities for preprocessing, integration, and visualization of single-cell and spatial transcriptomics data
Project description
grthub-tools
Utilities for single-cell and spatial transcriptomics workflows built around Scanpy/AnnData.
Installation
pip install grthub-tools
What is included
- Data loading helpers for 10x and Parse Biosciences outputs.
- Preprocessing utilities (QC, filtering, normalization, HVG workflows).
- Integration helpers using Harmony and scVI.
- Plotting helpers for common UMAP and metadata views.
Quick start
from grthub_tools import read_10x_data, preprocess_adata
adata = read_10x_data("/path/to/filtered_feature_bc_matrix")
adata = preprocess_adata(adata, n_top_genes=2000)
Development build with uv
uv build
Built artifacts are written to dist/.
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