Metadata-Version: 2.3
Name: grthub-tools
Version: 0.1.0
Summary: Utilities for preprocessing, integration, and visualization of single-cell and spatial transcriptomics data
Keywords: single-cell,scanpy,anndata,spatial-transcriptomics,scvi
Author: Kevin Stachelek
Author-email: Kevin Stachelek <kstachel@uci.edu>
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Dist: anndata>=0.10.9
Requires-Dist: harmonypy>=0.0.10
Requires-Dist: matplotlib>=3.9.4
Requires-Dist: numpy>=2.0.2
Requires-Dist: pandas>=2.3.2
Requires-Dist: scanpy>=1.10.3
Requires-Dist: scvi-tools>=1.0.0
Requires-Python: >=3.9
Project-URL: Homepage, https://github.com/whtns/grthub_tools
Project-URL: Issues, https://github.com/whtns/grthub_tools/issues
Description-Content-Type: text/markdown

# grthub-tools

Utilities for single-cell and spatial transcriptomics workflows built around Scanpy/AnnData.

## Installation

```bash
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

```python
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

```bash
uv build
```

Built artifacts are written to `dist/`.
