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This repository hosts the source code corresponding to the method described inNoël, F., Massenet-Regad, L., Carmi-Levy, I. et al. to infer intercellular communication networks and dissect intercellular communication between multiples cell types based on their transcriptomic profiles.

• Contains amanually curated ligand-receptor interactions database: curated exclusively fromhuman studies, ICELLNET database takes into account themultiple 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

• 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 on updates and previous versions can be foundhere.

Remark: ICELLNET v2.0.0 requires R version < 4.1. For latest R versions (> 4.1.x), please use ICELLNET v2.2.x.

• Detailed documentation
• ICELLNET analysis on scRNAseq data:Tutorial
• ICELLNET analysis on sorted cell-population transcriptomic data:
  • Script: analyze cell-cell communication between different cell populations from the same sample
  • Tutorial: 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).

install.packages(c("devtools", "jetset", "readxl", "psych", "GGally", "gplots", "ggplot2", "RColorBrewer", "data.table", "grid", "gridExtra", "ggthemes", "scales","rlist")) ##Installs devtools and the icellnet CRAN dependanciesif (!requireNamespace("BiocManager", quietly = TRUE)) # Installs icellnet Bioconductor dependancies     install.packages("BiocManager")BiocManager::install(c("BiocGenerics", "org.Hs.eg.db", "hgu133plus2.db", "annotate"))

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.

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

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-xlink

Massenet-Regad L, Soumelis V. ICELLNET v2: a versatile method for cell-cell communication analysis from human transcriptomic data. Bioinformatics. 2024 Mar 4;40(3):btae089. doi: 10.1093/bioinformatics/btae089. PMID: 38490248.link