{"id":24528973,"url":"https://github.com/saezlab/liana-py","last_synced_at":"2025-04-05T11:08:21.837Z","repository":{"id":63010402,"uuid":"539992330","full_name":"saezlab/liana-py","owner":"saezlab","description":"LIANA+: an all-in-one framework for cell-cell communication","archived":false,"fork":false,"pushed_at":"2024-07-18T11:49:07.000Z","size":234769,"stargazers_count":141,"open_issues_count":27,"forks_count":16,"subscribers_count":2,"default_branch":"main","last_synced_at":"2024-08-07T13:28:08.758Z","etag":null,"topics":["cell-cell-communication","ligand-receptor","python","single-cell","single-cell-rna-seq","spatial","spatialomics"],"latest_commit_sha":null,"homepage":"http://liana-py.readthedocs.io/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/saezlab.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2022-09-22T13:20:35.000Z","updated_at":"2024-08-08T15:02:39.161Z","dependencies_parsed_at":"2023-02-15T08:46:10.401Z","dependency_job_id":"39deae6b-652e-4154-854c-4fad254e2092","html_url":"https://github.com/saezlab/liana-py","commit_stats":{"total_commits":620,"total_committers":9,"mean_commits":68.88888888888889,"dds":0.04516129032258065,"last_synced_commit":"1543d165a7d6b682f8b2b2557216089a75450c98"},"previous_names":[],"tags_count":14,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2Fliana-py","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2Fliana-py/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2Fliana-py/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2Fliana-py/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/saezlab","download_url":"https://codeload.github.com/saezlab/liana-py/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":247325693,"owners_count":20920714,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["cell-cell-communication","ligand-receptor","python","single-cell","single-cell-rna-seq","spatial","spatialomics"],"created_at":"2025-01-22T07:34:15.084Z","updated_at":"2025-04-05T11:08:21.811Z","avatar_url":"https://github.com/saezlab.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# LIANA+: an all-in-one cell-cell communication framework \u003cimg src=\"https://raw.githubusercontent.com/saezlab/liana-py/dev/docs/source/_static/logo.png?raw=true\" align=\"right\" height=\"125\"\u003e\n\n\u003c!-- badges: start --\u003e\n[![main](https://github.com/saezlab/liana-py/actions/workflows/main.yml/badge.svg)](https://github.com/saezlab/liana-py/actions)\n[![GitHub issues](https://img.shields.io/github/issues/saezlab/liana-py.svg)](https://github.com/saezlab/liana-py/issues/)\n[![Documentation Status](https://readthedocs.org/projects/liana-py/badge/?version=latest)](https://liana-py.readthedocs.io/en/latest/?badge=latest)\n[![codecov](https://codecov.io/gh/saezlab/liana-py/branch/main/graph/badge.svg?token=TM0P29KKN5)](https://codecov.io/gh/saezlab/liana-py)\n[![Downloads](https://static.pepy.tech/badge/liana)](https://pepy.tech/project/liana)\n\u003c!-- badges: end --\u003e\n\nLIANA+ is a scalable framework that adapts 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) \u0026 [MuData](https://github.com/scverse/mudata) objects as input.\n\n\u003cimg src=\"https://raw.githubusercontent.com/saezlab/liana-py/main/docs/source/_static/abstract.png\" width=\"700\" align=\"center\"\u003e\n\n## Contributions\n\nWe welcome suggestions, ideas, and contributions! Please 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### 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#### Infer Metabolite-mediated CCC from transcriptomics?\n- [Non-spatial Data](https://liana-py.readthedocs.io/en/latest/notebooks/sc_multi.html#Metabolite-mediated-CCC-from-Transcriptomics-Data)\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., 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\n\nDimitrov, 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\n\nPlease also consider citing any of the methods and/or resources that were particularly relevant for your research!\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsaezlab%2Fliana-py","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsaezlab%2Fliana-py","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsaezlab%2Fliana-py/lists"}