{"id":24529054,"url":"https://github.com/saezlab/ligrec_decouple","last_synced_at":"2025-04-14T17:10:50.843Z","repository":{"id":77872768,"uuid":"377782555","full_name":"saezlab/ligrec_decouple","owner":"saezlab","description":"Systematic Comparison of Cell-Cell Communication Tools and 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Systematic Comparison of Cell-Cell Communication Tools and Resources\n\nRepository used to reproduce the results from [Comparison of Resources and Methods to infer Cell-Cell Communication from Single-cell RNA Data](https://www.biorxiv.org/content/10.1101/2021.05.21.445160v1)\n\n\n## LIANA Analysis Content\n\n### I) Descriptive Resource Analysis\nThe code to reproduce the descriptive analysis of resources can be found at:\n[analysis/resource_analysis](https://github.com/saezlab/ligrec_decouple/tree/main/analysis/resource_analysis)\n\n### II) Spatial Co-localization\nThe code to reproduce the co-localization analysis can be found at:\n[analysis/spatial](https://github.com/saezlab/ligrec_decouple/tree/main/analysis/spatial)\n\n### III) Cytokine Signalling Agreement\nThe code to reproduce the cytokine activity (/w [CytoSig](https://www.nature.com/articles/s41592-021-01274-5)) agreement analysis can be found at:\n[analysis/cytosig](https://github.com/saezlab/ligrec_decouple/tree/main/analysis/cytosig)\n\n### IV) CITE-Seq Correlation/Specificity\nThe code to reproduce the Correlation/Specificity analysis of methods with CITE-Seq can be found at:\n[analysis/citeseq](https://github.com/saezlab/ligrec_decouple/tree/main/analysis/citeseq)\n\n### V) Comparison of Methods and Resources\nThe code to reproduce the comparison between method-resource combinations can be found at:\n[analysis/comparison](https://github.com/saezlab/ligrec_decouple/tree/main/analysis/comparison)\n\n### VI) Robustness\nThe code to reproduce the robustness analyses can be found at:\n[analysis/robustness](https://github.com/saezlab/ligrec_decouple/tree/main/analysis/robustness)\n\n\n## Environment set-up\n# Clone repo\n```{bash}\ngit clone https://github.com/saezlab/ligrec_decouple\n```\n\nUse `analysis/initiate_environment.R` to restore the R environment used to produce the results in the publication.\n\nFinally, refer to [LIANA++](https://saezlab.github.io/liana/articles/liana_devel.html) for instructions how to set-up the LIANA environment used to call the different external tools.\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsaezlab%2Fligrec_decouple","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsaezlab%2Fligrec_decouple","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsaezlab%2Fligrec_decouple/lists"}