This repository hosts the source code corresponding to the method described in Noël, 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.

To install it, the easiest way is to use the R package devtools and its function install_github. If you don't have all the dependancies needed to use ICELLNET package, run the commands below:

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"))

Then you just have to load devtools package and run the command below:

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.
Examples on how to use icellnet package functions can be found in the Vignette.

Last package update: 2021-10-01

New on ICELLNET - 2021-07-21:

• ICELLNET ligand/receptor database include now 752 human ligand/receptor interactions, manually curated. In addition to immune checkpoints, cytokines, and chemokines, it now includes additional interactions from classified in an additional family "extracellular matrix", among others added interactions.
• New release (version 1.00): New graphical representations to handle cell-cell communication studies from single-cell RNAseq datasets. See Exemple2_scRNAseq.md for details.

New on ICELLNET - 2021-03-30:

• ICELLNET ligand/receptor database include now 543 human ligand/receptor interactions manually curated, with a particular interest on immune checkpoints, cytokines, and chemokines.
• ICELLNET includes now new features to handle cell-cell communication studies from single-cell RNAseq datasets. See Vignette and use case Exemple2_scRNAseq.md for details.