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

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

hca_anndata_tools-0.6.0.tar.gz (937.5 kB view details)

Uploaded Jul 10, 2026 Source

Built Distribution

If you're not sure about the file name format, learn more about wheel file names.

The dropdown lists show the available interpreters, ABIs, and platforms. Enable javascript to be able to filter the list of wheel files.

hca_anndata_tools-0.6.0-py3-none-any.whl (947.5 kB view details)

Uploaded Jul 10, 2026 Python 3

File details

Details for the file hca_anndata_tools-0.6.0.tar.gz.

File metadata

Download URL: hca_anndata_tools-0.6.0.tar.gz
Upload date: Jul 10, 2026
Size: 937.5 kB
Tags: Source
Uploaded using Trusted Publishing? Yes
Uploaded via: twine/6.1.0 CPython/3.13.12

File hashes

Hashes for hca_anndata_tools-0.6.0.tar.gz
Algorithm	Hash digest
SHA256	`2190cbe3e35f9be22a524c08a0153b087acd926aa076de3f1e5614b606cdbcc5`
MD5	`bc390af9615d2d5317eeb8fda83cb09e`
BLAKE2b-256	`3e2eb4930000f888f1b4c0533f56afb6308824521cb47a9462bf384da28b81a5`

See more details on using hashes here.

Provenance

The following attestation bundles were made for hca_anndata_tools-0.6.0.tar.gz:

Publisher: release-please.yml on clevercanary/hca-validation-tools

Attestations: Values shown here reflect the state when the release was signed and may no longer be current.

Statement:
- Statement type: https://in-toto.io/Statement/v1
- Predicate type: https://docs.pypi.org/attestations/publish/v1
- Subject name: hca_anndata_tools-0.6.0.tar.gz
- Subject digest: 2190cbe3e35f9be22a524c08a0153b087acd926aa076de3f1e5614b606cdbcc5
- Sigstore transparency entry: 2136282257
- Sigstore integration time: Jul 10, 2026
Source repository:
- Permalink: clevercanary/hca-validation-tools@400451d36be5cc8fdba3a7d29d33be9871db6e14
- Branch / Tag: refs/heads/main
- Owner: https://github.com/clevercanary
- Access: public
Publication detail:
- Token Issuer: https://token.actions.githubusercontent.com
- Runner Environment: github-hosted
- Publication workflow: release-please.yml@400451d36be5cc8fdba3a7d29d33be9871db6e14
- Trigger Event: push