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Dissection of intercellular communication using the transcriptome-based framework ICELLNET

Floriane Noël and Lucile Massenet-Regad

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.

Package installation

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.

ICELLNET news:

Last package update: 2023-06-29 (v1.3.0)

Last ligand-receptor database update: 2022-06-15

New on ICELLNET (v1.2.0) - 2023-02-05: ICELLNET can now handle spatial transcriptomic data!

New on ICELLNET - 2022-06-15: ICELLNET database has been expanded to 1034 interactions, focusing on adding tumor microenvironment related interactions.

New on ICELLNET (v1.0.0) - 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 1.0.0): 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.