https://github.com/saezlab/ligrec_decouple
Systematic Comparison of Cell-Cell Communication Tools and Resources
https://github.com/saezlab/ligrec_decouple
Last synced: over 1 year ago
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Systematic Comparison of Cell-Cell Communication Tools and Resources
- Host: GitHub
- URL: https://github.com/saezlab/ligrec_decouple
- Owner: saezlab
- License: gpl-3.0
- Created: 2021-06-17T09:54:38.000Z (about 5 years ago)
- Default Branch: main
- Last Pushed: 2022-05-09T07:01:56.000Z (about 4 years ago)
- Last Synced: 2025-03-28T05:51:01.784Z (over 1 year ago)
- Language: R
- Size: 5.99 MB
- Stars: 6
- Watchers: 3
- Forks: 0
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Systematic Comparison of Cell-Cell Communication Tools and Resources
Repository 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)
## LIANA Analysis Content
### I) Descriptive Resource Analysis
The code to reproduce the descriptive analysis of resources can be found at:
[analysis/resource_analysis](https://github.com/saezlab/ligrec_decouple/tree/main/analysis/resource_analysis)
### II) Spatial Co-localization
The code to reproduce the co-localization analysis can be found at:
[analysis/spatial](https://github.com/saezlab/ligrec_decouple/tree/main/analysis/spatial)
### III) Cytokine Signalling Agreement
The code to reproduce the cytokine activity (/w [CytoSig](https://www.nature.com/articles/s41592-021-01274-5)) agreement analysis can be found at:
[analysis/cytosig](https://github.com/saezlab/ligrec_decouple/tree/main/analysis/cytosig)
### IV) CITE-Seq Correlation/Specificity
The code to reproduce the Correlation/Specificity analysis of methods with CITE-Seq can be found at:
[analysis/citeseq](https://github.com/saezlab/ligrec_decouple/tree/main/analysis/citeseq)
### V) Comparison of Methods and Resources
The code to reproduce the comparison between method-resource combinations can be found at:
[analysis/comparison](https://github.com/saezlab/ligrec_decouple/tree/main/analysis/comparison)
### VI) Robustness
The code to reproduce the robustness analyses can be found at:
[analysis/robustness](https://github.com/saezlab/ligrec_decouple/tree/main/analysis/robustness)
## Environment set-up
# Clone repo
```{bash}
git clone https://github.com/saezlab/ligrec_decouple
```
Use `analysis/initiate_environment.R` to restore the R environment used to produce the results in the publication.
Finally, 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.