This release is a pre-release and may not be stable for production use.
SIGMA (sigma-omics)
SIGMA is a Python toolkit for spatial interface analysis integrating mass-spectrometry imaging (MSI) and spatial transcriptomic representations.
This package is currently an alpha release. Its scientific definitions are preserved from the HBC515 reference implementation while the API and multi-dataset validation are being completed.
Install
After the first PyPI release:
pip install sigma-omics
The distribution name is sigma-omics; the Python import remains
sigma_spatial.
Install from source
pip install -e .
Minimal usage
import scanpy as sc
from sigma_spatial import SIGMA
adata = sc.read_h5ad("sample.h5ad")
SIGMA(seed=0).fit(
adata,
annotation_key="annotation",
tumor_label="Tumor",
stroma_label="Stroma",
rna_key="X_harmony",
)
# Main outputs
adata.obs[["sigma_region_probability", "sigma_boundary", "sigma_d_signed"]]
Scope
The package should contain reusable SIGMA computation only. Manuscript-specific simulation, benchmarking, GO enrichment, plotting, and sample-specific analyses should live under examples/ or a separate analysis repository.
1 maintainer
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
Filter files by name, interpreter, ABI, and platform.
If you're not sure about the file name format, learn more about wheel file names.
Copy a direct link to the current filters
File details
Details for the file sigma_omics-0.1.0a1.tar.gz.
File metadata
- Download URL: sigma_omics-0.1.0a1.tar.gz
- Upload date:
- Size: 16.5 kB
- Tags: Source
- Uploaded using Trusted Publishing? Yes
- Uploaded via:
twine/7.0.0 CPython/3.13.14
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 |
d16a17d404f095a401192d2bf4d2645749b9cc85fb7fa1185d0fd56d1972093d
|
|
| MD5 |
ff456c5444c956cae56f3c27bb9c9321
|
|
| BLAKE2b-256 |
09436b03ce70aec0354cdf6faab18f314807da04e1ca2a71fb610127306984ee
|
Provenance
The following attestation bundles were made for sigma_omics-0.1.0a1.tar.gz:
Publisher:
publish.yml on Elsa-bingxue/SIGMA
-
Statement:
-
Statement type:
https://in-toto.io/Statement/v1 -
Predicate type:
https://docs.pypi.org/attestations/publish/v1 -
Subject name:
sigma_omics-0.1.0a1.tar.gz -
Subject digest:
d16a17d404f095a401192d2bf4d2645749b9cc85fb7fa1185d0fd56d1972093d - Sigstore transparency entry: 2498537332
- Sigstore integration time:
-
Permalink:
Elsa-bingxue/SIGMA@15e765a1521a07687527350c8ac8f24540937119 -
Branch / Tag:
refs/tags/v0.1.0a1 - Owner: https://github.com/Elsa-bingxue
-
Access:
public
-
Token Issuer:
https://token.actions.githubusercontent.com -
Runner Environment:
github-hosted -
Publication workflow:
publish.yml@15e765a1521a07687527350c8ac8f24540937119 -
Trigger Event:
release
-
Statement type:
File details
Details for the file sigma_omics-0.1.0a1-py3-none-any.whl.
File metadata
- Download URL: sigma_omics-0.1.0a1-py3-none-any.whl
- Upload date:
- Size: 13.4 kB
- Tags: Python 3
- Uploaded using Trusted Publishing? Yes
- Uploaded via:
twine/7.0.0 CPython/3.13.14
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 |
b64cf825e819abfe34d27e412bcaef3763f3f25b82e4380db50b6541811c96cf
|
|
| MD5 |
6bb263894170f93a61e2d4b466177e81
|
|
| BLAKE2b-256 |
f2a62eaf36422bea7688650793519b80da6c7443cc6a922865c419063f0f55ff
|
Provenance
The following attestation bundles were made for sigma_omics-0.1.0a1-py3-none-any.whl:
Publisher:
publish.yml on Elsa-bingxue/SIGMA
-
Statement:
-
Statement type:
https://in-toto.io/Statement/v1 -
Predicate type:
https://docs.pypi.org/attestations/publish/v1 -
Subject name:
sigma_omics-0.1.0a1-py3-none-any.whl -
Subject digest:
b64cf825e819abfe34d27e412bcaef3763f3f25b82e4380db50b6541811c96cf - Sigstore transparency entry: 2498537336
- Sigstore integration time:
-
Permalink:
Elsa-bingxue/SIGMA@15e765a1521a07687527350c8ac8f24540937119 -
Branch / Tag:
refs/tags/v0.1.0a1 - Owner: https://github.com/Elsa-bingxue
-
Access:
public
-
Token Issuer:
https://token.actions.githubusercontent.com -
Runner Environment:
github-hosted -
Publication workflow:
publish.yml@15e765a1521a07687527350c8ac8f24540937119 -
Trigger Event:
release
-
Statement type:
