hca-anndata-tools

Library for inspection, summarization, and statistics of AnnData h5ad files.

Installation

pip install hca-anndata-tools

Usage

from hca_anndata_tools import get_summary, get_descriptive_stats, locate_files

# Find h5ad files
files = locate_files("/path/to/data")

# Get structural overview
summary = get_summary("/path/to/my_atlas.h5ad")

# Get column statistics
stats = get_descriptive_stats("/path/to/my_atlas.h5ad", columns=["cell_type"], value_counts=True)

API

locate_files - Find all .h5ad files in a directory
get_summary - Structural overview: cell/gene counts, columns, embeddings, layers
get_storage_info - HDF5 compression, chunking, sparse format details
get_descriptive_stats - Descriptive statistics and value counts for obs/var columns
view_data - View slices of any attribute (obs, var, X, obsm, uns, etc.)
plot_embedding - UMAP/PCA scatter plots as base64 PNG
get_cap_annotations - Inspect CAP cell annotation metadata

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