{"id":24528934,"url":"https://github.com/saezlab/liana","last_synced_at":"2025-04-07T16:18:53.629Z","repository":{"id":40507201,"uuid":"333499249","full_name":"saezlab/liana","owner":"saezlab","description":"LIANA: a LIgand-receptor ANalysis frAmework","archived":false,"fork":false,"pushed_at":"2024-08-07T06:58:03.000Z","size":86310,"stargazers_count":196,"open_issues_count":37,"forks_count":33,"subscribers_count":8,"default_branch":"master","last_synced_at":"2025-03-31T13:18:25.970Z","etag":null,"topics":["cell-cell-communication","cellchat","cellphonedb","liana","ligand-receptor","omnipath"],"latest_commit_sha":null,"homepage":"https://saezlab.github.io/liana/","language":"R","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":"NEWS.md","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":"2021-01-27T17:01:04.000Z","updated_at":"2025-03-13T08:55:05.000Z","dependencies_parsed_at":"2023-02-19T09:16:08.523Z","dependency_job_id":"8e0c7c34-e8da-4bb9-88a0-4f75ae19ef6e","html_url":"https://github.com/saezlab/liana","commit_stats":null,"previous_names":[],"tags_count":6,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2Fliana","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2Fliana/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2Fliana/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2Fliana/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/saezlab","download_url":"https://codeload.github.com/saezlab/liana/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":247685628,"owners_count":20979085,"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","cellchat","cellphonedb","liana","ligand-receptor","omnipath"],"created_at":"2025-01-22T07:34:08.793Z","updated_at":"2025-04-07T16:18:53.602Z","avatar_url":"https://github.com/saezlab.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"\u003c!-- badges: start --\u003e\n[![R-CMD-check](https://github.com/saezlab/liana/workflows/R-CMD-check/badge.svg)](https://github.com/saezlab/liana/actions)\n\u003c!-- badges: end --\u003e\n\n# LIANA: a LIgand-receptor ANalysis frAmework \u003cimg src=\"https://www.dropbox.com/s/ecrxuy5f6ccdvl0/liana_small.png?raw=1\" align=\"right\"\u003e\n    \nLIANA enables the use of any combination of ligand-receptor methods and resources, and their consensus. The faster, memory-efficient, and more comprehensive LIANA+ framework is available [here](https://github.com/saezlab/liana-py).\n    \n## Install LIANA  \n```r\nif (!requireNamespace(\"BiocManager\", quietly = TRUE))\n    install.packages(\"BiocManager\")\n\nif (!requireNamespace(\"remotes\", quietly = TRUE))\n    install.packages(\"remotes\")\n\nremotes::install_github('saezlab/liana')\n```\n\n  \n## Tutorial\nSee a [tutorial](https://saezlab.github.io/liana/articles/liana_tutorial.html) how to use LIANA to run any combination of 7 methods, plus their consensus, and 16 different resources!\nThe tutorial with the test data takes minutes to complete!    \n  \nAdditional tutorials:  \n\n* [LIANA across Conditions with cell2cell-Tensor](https://ccc-protocols.readthedocs.io/en/latest/). To setup an environment with Tensor-cell2cell and LIANA, please follow the instructions here: https://github.com/saezlab/ccc_protocols/tree/main/env_setup \n\n* [How to combine LIANA and NicheNet](https://saezlab.github.io/liana/articles/liana_nichenet.html)  \n\n* [How to make use of OmniPathR's intracellular component](https://saezlab.github.io/liana/articles/liana_intracell.html)  \n\n* [How to convert the resources in LIANA to orthologs from other species](https://saezlab.github.io/liana/articles/liana_ortho.html)\n\n* [LIANA for developers and benchmarks](https://saezlab.github.io/liana/articles/liana_devel.html)  \n  \n\nWe also refer users to the Cell-cell communication chapter in the [best-practices book from Theis lab](https://github.com/theislab/single-cell-best-practices), as it provides an overview of the common limitations and assumptions in CCC inference from (single-cell) transcriptomics data.\n\n  \n## LIANA Framework\n\nThe continuous developments of single-cell RNA-Seq (scRNA-Seq) have sparked\nan immense interest in understanding intercellular crosstalk. Multiple\ntools and resources that aid the investigation of cell-cell communication (CCC)\nwere published recently.\nHowever, these methods and resources are usually in a fixed combination of a\ntool and its corresponding resource, but in principle any resource could be\ncombined with any method.  \n\n\nTo this end, we built a framework to decouple the methods from their corresponding resources.\n   \nLIANA also goes a step further as it provides:\n\n* A robust and extendable architecture that aims to accelerate method development and benchmarks\n\n* A rank aggregate from the results of different methods\n\n* A customizable plethora of resources\n  \n![landingpage](vignettes/ligrec_pipe.png)\n  \n  \n## Tools\n\nThe tools implemented in this repository are:\n\n- [CellPhoneDBv2](https://github.com/Teichlab/cellphonedb) (*, $)\n- [CellChat](https://github.com/sqjin/CellChat)\n- [NATMI](https://github.com/forrest-lab/NATMI) (*, $)\n- [Connectome](https://github.com/msraredon/Connectome) (`edge_weights`) (*, $)\n- [SingleCellSignalR](https://github.com/SCA-IRCM/SingleCellSignalR) (`LRscores`) (SCA) (*, $)\n- [iTALK](https://github.com/Coolgenome/iTALK)-inspired *1-vs-rest* LogFC score (`logfc_comb`) (*, $)\n- [CytoTalk](https://advances.sciencemag.org/content/7/16/eabf1356)-inspired `cross-talk` scores (*)\n  \n- `consensus_rank` of the predictions is also provided using the [RobustRankAggregate](https://pubmed.ncbi.nlm.nih.gov/22247279/) method\n  \n  \n*The scoring systems from these methods were re-implemented in LIANA in order to account for multi-meric complexes, simplify the calls to the individual pipelines, or reduce any possible inconsistencies and redundancies in their downstream integration. If you wish to run LIANA with the original tools please see [LIANA++](https://saezlab.github.io/liana/articles/liana_devel.html).\n  \n$ Default methods in LIANA.\n\n  \n## Resources\n\n### Cell-cell Communication resources\n\nThe following CCC resources are accessible via this pipeline:\n\n- *Consensus*\n\n- CellCall\n- CellChatDB\n- CellPhoneDB\n- Ramilowski2015\n- Baccin2019\n- LRdb\n- Kiroauc2010\n- ICELLNET\n- iTALK\n- EMBRACE\n- HPMR\n- Guide2Pharma\n- ConnectomeDB2020\n- CellTalkDB\n- OmniPath [Deprecated]\n  \n  \n### Consensus Resource\nLIANA's default resource was generated from the `Consensus` of several expert-curated resources, then\nfiltered to additional quality control steps including literature support, complex re-union/consensus, and localisation.\n\n  \n### OmniPath\n  \nAll the resources above are retrieved from [OmniPath](https://omnipathdb.org/),\nand more specifically [OmnipathR](https://github.com/saezlab/OmnipathR).\nHowever, individual resources retrieved from the OmniPath web service are not to be affected by this,\nas each resource expected to be identical to its original form, apart from minor processing steps.\n  \n`OmniPath` itself serves as a composite CCC resource combining all the ones listed\nabove + [more](https://doi.org/10.15252/msb.20209923). `OmniPath` also collects\nfurther information about the roles and localisation of proteins in intercellular communication.\n\nWe made use of this information to generate the `Consensus` resource.\nTo obtain more information how we filtered the default `Consensus` resource,\nas well as to explore custom filter options see [customizing OmniPath resources](https://saezlab.github.io/liana/articles/liana_custom_op.html).  \n  \n  \n## LIANA++\nIf you are interested in making use of the LIANA architecture for your own method, [this vignette](https://saezlab.github.io/liana/articles/liana_devel.html) provides instructions how to obtain a comprehensive table of LR statistics, which can then be used by custom scoring functions.\nIn the [same vignette](https://saezlab.github.io/liana/articles/liana_devel.html) are also instructions how to install and run the original methods via a convenient R wrapper, e.g. for their benchmark.\n  \n\n  \n## Contact\nWe appreciate any feedback, so please do not hesitate to open an issue on the [liana github page](https://github.com/saezlab/liana)!  \n  \n  \n  \n## NEWS\n\n\u003cstrong\u003e We are commited to the further development of LIANA and we refer the users to \nthe [NEWS page](https://github.com/saezlab/liana/blob/master/NEWS.md)! \u003c/strong\u003e\n  \n  \n### Citing `LIANA`:\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.\n*Nat Commun 13*, 3224 (2022). [https://doi.org/10.1038/s41467-022-30755-0](https://www.nature.com/articles/s41467-022-30755-0)\n\n#### Also, if you use the `OmniPath` CCC Resource for your analysis, please cite:\nTürei, D., Valdeolivas, A., Gul, L., Palacio‐Escat, N., Klein, M., Ivanova, O., Ölbei, M., Gábor, A., Theis, F., Módos, D. and Korcsmáros, T., 2021. Integrated intra‐and intercellular signaling knowledge for multicellular omics analysis. Molecular systems biology, 17(3), p.e9923.\nhttps://doi.org/10.15252/msb.20209923\n  \n#### Similarly, please consider citing any of the methods and/or resources implemented in liana, that were particularly relevant for your research!\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsaezlab%2Fliana","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsaezlab%2Fliana","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsaezlab%2Fliana/lists"}