https://github.com/soumelis-lab/ICELLNET

https://github.com/soumelis-lab/ICELLNET

Last synced: 4 months ago
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• Host: GitHub
• URL: https://github.com/soumelis-lab/ICELLNET
• Owner: soumelis-lab
• Created: 2020-03-04T14:08:09.000Z (over 4 years ago)
• Default Branch: master
• Last Pushed: 2023-11-20T18:53:10.000Z (7 months ago)
• Last Synced: 2023-11-20T19:54:49.689Z (7 months ago)
• Language: R
• Size: 101 MB
• Stars: 13
• Watchers: 2
• Forks: 8
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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• awesome-cell-cell-communication - iCELLNET - [R]- iCELLNET enables dissection of intercellular communication using the transcriptome-based framework. (Uncategorized / Uncategorized)

README

        

# Dissection of intercellular communication using the transcriptome-based framework ICELLNET

This repository hosts the source code corresponding to the method described in [Noël, F., Massenet-Regad, L., Carmi-Levy, I. et al. ](https://www.nature.com/articles/s41467-021-21244-x) to infer intercellular communication networks and dissect intercellular communication between multiples cell types based on their transcriptomic profiles.

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## ICELLNET key features: 

- Contains a *manually curated ligand-receptor interactions database*: curated exclusively from *human* studies, ICELLNET database takes into account the *multiple* subunits of ligand and receptor complexes (more than 1600 interactions)

- *Versatile* tool applicable on a wide range of transcriptomic technologies (microarray, bulk RNAseq, scRNAseq, spatial transcriptomics)

- Several visualization modes of cell-cell communication analysis results

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## New on ICELLNET v2.0.0 

- New structure and extension of ICELLNET database up to 1669 interactions.

- Possibility to ICELLNET analysis using other databases such as CellPhoneDB as input

- Updates of several functions to match the new structure of ICELLNET database.

Additional details and previous updates can be found [here](https://github.com/soumelis-lab/ICELLNET/blob/master/UPDATES.md).

## Information related to ICELLNET and tutorials

- [Detailed documentation](https://github.com/soumelis-lab/ICELLNET/blob/master/Vignette.md)

- ICELLNET analysis on scRNAseq data: [Tutorial](https://github.com/soumelis-lab/ICELLNET/blob/master/exemples_tutorials/Exemple2_scRNAseq.md) 

- ICELLNET analysis on sorted cell-population transcriptomic data: 

  - [Script](https://github.com/soumelis-lab/ICELLNET/issues/12): analyze cell-cell communication between different cell populations from the same sample

  - [Tutorial](https://github.com/soumelis-lab/ICELLNET/blob/master/exemples_tutorials/Exemple1_CAF.md):  infer cell-cell communication from the transcriptome of a single cell type of interest with the Primary Cell Atlas (Database of reference transcriptome of 33 cell types). 

  

## Installation

### Installation of dependencies:

    install.packages(c("devtools", "jetset", "readxl", "psych", "GGally", "gplots", "ggplot2", "RColorBrewer", "data.table", "grid", "gridExtra", "ggthemes", "scales","rlist")) ##Installs devtools and the icellnet CRAN dependancies

    if (!requireNamespace("BiocManager", quietly = TRUE)) # Installs icellnet Bioconductor dependancies 

        install.packages("BiocManager")

    BiocManager::install(c("BiocGenerics", "org.Hs.eg.db", "hgu133plus2.db", "annotate"))

    

### Installation of ICELLNET package:

    library(devtools)

    install_github("soumelis-lab/ICELLNET",ref="master", subdir="icellnet")

Once all the dependencies are downloaded and loaded, you can load the ‘icellnet’ package.    

## Citation

If you use our human curated ligand-receptor interaction database or the ICELLNET method, please cite our paper: 

Noël, F., Massenet-Regad, L., Carmi-Levy, I. et al. Dissection of intercellular communication using the transcriptome-based framework ICELLNET. Nat Commun 12, 1089 (2021). https://doi.org/10.1038/s41467-021-21244-x [link](https://www.nature.com/articles/s41467-021-21244-x)