| Name | liana JSON |
| Version |
1.4.0
JSON |
| download |
| home_page | https://liana-py.readthedocs.io |
| Summary | LIANA+: a one-stop-shop framework for cell-cell communication |
| upload_time | 2024-09-02 10:24:03 |
| maintainer | None |
| docs_url | None |
| author | Daniel Dimitrov |
| requires_python | <3.12,>=3.8 |
| license | GPLv3 |
| keywords |
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# LIANA+: an all-in-one cell-cell communication framework <img src="https://raw.githubusercontent.com/saezlab/liana-py/dev/docs/source/_static/logo.png?raw=true" align="right" height="125">
<!-- badges: start -->
[](https://github.com/saezlab/liana-py/actions)
[](https://github.com/saezlab/liana-py/issues/)
[](https://liana-py.readthedocs.io/en/latest/?badge=latest)
[](https://codecov.io/gh/saezlab/liana-py)
[](https://pepy.tech/project/liana)
<!-- badges: end -->
LIANA+ is a scalable framework that integrates and extends existing methods and knowledge to study cell-cell communication in single-cell, spatially-resolved, and multi-modal omics data. It is part of the [scverse ecosystem](https://github.com/scverse), and relies on [AnnData](https://github.com/scverse/anndata) & [MuData](https://github.com/scverse/mudata) objects as input.
<img src="https://raw.githubusercontent.com/saezlab/liana-py/main/docs/source/_static/abstract.png" width="700" align="center">
## Development & Contributions
We welcome suggestions, ideas, and contributions! Please use do not hesitate to contact us, open issues, and check the [contributions guide](https://liana-py.readthedocs.io/en/latest/contributing.html).
## Vignettes
A set of extensive vignettes can be found in the [LIANA+ documentation](https://liana-py.readthedocs.io/en/latest/).
## Decision Tree
### Q: Does the data contain spatial coordinates?
#### Yes
- **Q: Bivariate or unsupervised, multi-variate, and multi-view analysis?**
- **Bivariate:**
- **Q: Are you interested in identifying the subregions of interactions (i.e., local interactions)?**
- **Yes:** Check the [**Local** Bivariate Metrics](https://liana-py.readthedocs.io/en/latest/notebooks/bivariate.html#Bivariate-Ligand-Receptor-Relationships)
- **No:** Check the [**Global** Bivariate Metrics](https://liana-py.readthedocs.io/en/latest/notebooks/bivariate.html#Bivariate-Ligand-Receptor-Relationships)
- **Unsupervised:** [Multi-view learning](https://liana-py.readthedocs.io/en/latest/notebooks/misty.html)
#### No
- **Q: Are you interested in comparing CCC across samples?**
- **Yes:**
- **Q: Are you interested in a specific contrast?**
- **Yes:** [Differential Contrasts and Downstream Signalling](https://liana-py.readthedocs.io/en/latest/notebooks/targeted.html)
- **No:** Unsupervised Cross-conditional LR inference with [MOFA+](https://liana-py.readthedocs.io/en/latest/notebooks/mofatalk.html) or [Tensor-cell2cell](https://liana-py.readthedocs.io/en/latest/notebooks/liana_c2c.html)
- **No:** [Steady-state Ligand-Receptor inference](https://liana-py.readthedocs.io/en/latest/notebooks/basic_usage.html)
### Is your data Multi-modal?
- **Spatial:** [Integrating Multi-Modal Spatially-Resolved Technologies](https://liana-py.readthedocs.io/en/latest/notebooks/sma.html)
- **Non-Spatial:** [Integrating Multi-Modal Single-Cell Technologies](https://liana-py.readthedocs.io/en/latest/notebooks/sc_multi.html)
## API
For further information please check LIANA's [API documentation](https://liana-py.readthedocs.io/en/latest/api.html).
## Cite LIANA+:
Dimitrov D., Schäfer P.S.L, Farr E., Rodriguez Mier P., Lobentanzer S., Badia-i-Mompel P., Dugourd A., Tanevski J., Ramirez Flores R.O. and Saez-Rodriguez J. LIANA+ provides an all-in-one framework for cell–cell communication inference. Nat Cell Biol (2024). https://doi.org/10.1038/s41556-024-01469-w
Dimitrov, D., Türei, D., Garrido-Rodriguez M., Burmedi P.L., Nagai, J.S., Boys, C., Flores, R.O.R., Kim, H., Szalai, B., Costa, I.G., Valdeolivas, A., Dugourd, A. and Saez-Rodriguez, J. Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data. Nat Commun 13, 3224 (2022). https://doi.org/10.1038/s41467-022-30755-0
Similarly, please consider citing any of the methods and/or resources implemented in liana, that were particularly relevant for your research!
Raw data
{
"_id": null,
"home_page": "https://liana-py.readthedocs.io",
"name": "liana",
"maintainer": null,
"docs_url": null,
"requires_python": "<3.12,>=3.8",
"maintainer_email": null,
"keywords": null,
"author": "Daniel Dimitrov",
"author_email": "daniel.dimitrov@uni-heidelberg.de",
"download_url": "https://files.pythonhosted.org/packages/41/52/10dd32e41ace0af919b9b9bcfd1706bb6cb94c9c7a5023d7c37ea4b88842/liana-1.4.0.tar.gz",
"platform": null,
"description": "# LIANA+: an all-in-one cell-cell communication framework <img src=\"https://raw.githubusercontent.com/saezlab/liana-py/dev/docs/source/_static/logo.png?raw=true\" align=\"right\" height=\"125\">\n\n<!-- badges: start -->\n[](https://github.com/saezlab/liana-py/actions)\n[](https://github.com/saezlab/liana-py/issues/)\n[](https://liana-py.readthedocs.io/en/latest/?badge=latest)\n[](https://codecov.io/gh/saezlab/liana-py)\n[](https://pepy.tech/project/liana)\n<!-- badges: end -->\n\nLIANA+ is a scalable framework that integrates and extends existing methods and knowledge to study cell-cell communication in single-cell, spatially-resolved, and multi-modal omics data. It is part of the [scverse ecosystem](https://github.com/scverse), and relies on [AnnData](https://github.com/scverse/anndata) & [MuData](https://github.com/scverse/mudata) objects as input.\n\n<img src=\"https://raw.githubusercontent.com/saezlab/liana-py/main/docs/source/_static/abstract.png\" width=\"700\" align=\"center\">\n\n## Development & Contributions\n\nWe welcome suggestions, ideas, and contributions! Please use do not hesitate to contact us, open issues, and check the [contributions guide](https://liana-py.readthedocs.io/en/latest/contributing.html).\n\n## Vignettes\nA set of extensive vignettes can be found in the [LIANA+ documentation](https://liana-py.readthedocs.io/en/latest/).\n\n## Decision Tree\n### Q: Does the data contain spatial coordinates?\n#### Yes\n- **Q: Bivariate or unsupervised, multi-variate, and multi-view analysis?**\n - **Bivariate:**\n - **Q: Are you interested in identifying the subregions of interactions (i.e., local interactions)?**\n - **Yes:** Check the [**Local** Bivariate Metrics](https://liana-py.readthedocs.io/en/latest/notebooks/bivariate.html#Bivariate-Ligand-Receptor-Relationships)\n - **No:** Check the [**Global** Bivariate Metrics](https://liana-py.readthedocs.io/en/latest/notebooks/bivariate.html#Bivariate-Ligand-Receptor-Relationships)\n - **Unsupervised:** [Multi-view learning](https://liana-py.readthedocs.io/en/latest/notebooks/misty.html)\n\n#### No\n- **Q: Are you interested in comparing CCC across samples?**\n - **Yes:**\n - **Q: Are you interested in a specific contrast?**\n - **Yes:** [Differential Contrasts and Downstream Signalling](https://liana-py.readthedocs.io/en/latest/notebooks/targeted.html)\n - **No:** Unsupervised Cross-conditional LR inference with [MOFA+](https://liana-py.readthedocs.io/en/latest/notebooks/mofatalk.html) or [Tensor-cell2cell](https://liana-py.readthedocs.io/en/latest/notebooks/liana_c2c.html)\n - **No:** [Steady-state Ligand-Receptor inference](https://liana-py.readthedocs.io/en/latest/notebooks/basic_usage.html)\n\n### Is your data Multi-modal?\n- **Spatial:** [Integrating Multi-Modal Spatially-Resolved Technologies](https://liana-py.readthedocs.io/en/latest/notebooks/sma.html)\n- **Non-Spatial:** [Integrating Multi-Modal Single-Cell Technologies](https://liana-py.readthedocs.io/en/latest/notebooks/sc_multi.html)\n\n## API\nFor further information please check LIANA's [API documentation](https://liana-py.readthedocs.io/en/latest/api.html).\n\n## Cite LIANA+:\n\nDimitrov D., Sch\u00e4fer P.S.L, Farr E., Rodriguez Mier P., Lobentanzer S., Badia-i-Mompel P., Dugourd A., Tanevski J., Ramirez Flores R.O. and Saez-Rodriguez J. LIANA+ provides an all-in-one framework for cell\u2013cell communication inference. Nat Cell Biol (2024). https://doi.org/10.1038/s41556-024-01469-w\n\nDimitrov, D., T\u00fcrei, D., Garrido-Rodriguez M., Burmedi P.L., Nagai, J.S., Boys, C., Flores, R.O.R., Kim, H., Szalai, B., Costa, I.G., Valdeolivas, A., Dugourd, A. and Saez-Rodriguez, J. Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data. Nat Commun 13, 3224 (2022). https://doi.org/10.1038/s41467-022-30755-0\n\nSimilarly, please consider citing any of the methods and/or resources implemented in liana, that were particularly relevant for your research!\n\n",
"bugtrack_url": null,
"license": "GPLv3",
"summary": "LIANA+: a one-stop-shop framework for cell-cell communication",
"version": "1.4.0",
"project_urls": {
"Homepage": "https://liana-py.readthedocs.io",
"Repository": "https://github.com/saezlab/liana-py"
},
"split_keywords": [],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "f35c9752bacdd5e1ceed3dec135d7c276ce87023bdc2cc38953654d1b7a620d3",
"md5": "210fcfa994cca9ec65148bc2451ecbb8",
"sha256": "4382b1bcbde39e6dfeb265703ecda59d6942656a6fcf6789b39e83a6b2a9c649"
},
"downloads": -1,
"filename": "liana-1.4.0-py3-none-any.whl",
"has_sig": false,
"md5_digest": "210fcfa994cca9ec65148bc2451ecbb8",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": "<3.12,>=3.8",
"size": 1172046,
"upload_time": "2024-09-02T10:23:57",
"upload_time_iso_8601": "2024-09-02T10:23:57.565393Z",
"url": "https://files.pythonhosted.org/packages/f3/5c/9752bacdd5e1ceed3dec135d7c276ce87023bdc2cc38953654d1b7a620d3/liana-1.4.0-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "415210dd32e41ace0af919b9b9bcfd1706bb6cb94c9c7a5023d7c37ea4b88842",
"md5": "3ddddd0277042b288de83f34714ce6af",
"sha256": "1172a9bef67ee22d5eb3f27144c61dddec3122bd515b131c9ed5b0529fcbf2d1"
},
"downloads": -1,
"filename": "liana-1.4.0.tar.gz",
"has_sig": false,
"md5_digest": "3ddddd0277042b288de83f34714ce6af",
"packagetype": "sdist",
"python_version": "source",
"requires_python": "<3.12,>=3.8",
"size": 1132447,
"upload_time": "2024-09-02T10:24:03",
"upload_time_iso_8601": "2024-09-02T10:24:03.641598Z",
"url": "https://files.pythonhosted.org/packages/41/52/10dd32e41ace0af919b9b9bcfd1706bb6cb94c9c7a5023d7c37ea4b88842/liana-1.4.0.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2024-09-02 10:24:03",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "saezlab",
"github_project": "liana-py",
"travis_ci": false,
"coveralls": false,
"github_actions": true,
"lcname": "liana"
}
