文件列表:

UPDATES.md (3751, 2023-11-20)
Vignette.md (20055, 2023-11-20)
data/ (0, 2023-11-20)
data/ICELLNETdb.csv (92954, 2023-11-20)
data/ICELLNETdb.tsv (92954, 2023-11-20)
data/PC.data.all.csv.zip (47328452, 2023-11-20)
data/PC.target.all.csv (179101, 2023-11-20)
data_CAF/ (0, 2023-11-20)
data_CAF/data_CAF.txt (12277044, 2023-11-20)
data_CAF/target_CAF.txt (1785, 2023-11-20)
exemples_tutorials/ (0, 2023-11-20)
exemples_tutorials/Code_SeuratObject_Exemple2.md (1898, 2023-11-20)
exemples_tutorials/Exemple1_CAF.md (11910, 2023-11-20)
exemples_tutorials/Exemple2_scRNAseq.md (12335, 2023-11-20)
exemples_tutorials/Exemple_ICELLNET_on bulk_RNAseq.R (2096, 2023-11-20)
exemples_tutorials/pictures/ (0, 2023-11-20)
exemples_tutorials/pictures/ICELLNET_CAF_balloon.png (158691, 2023-11-20)
exemples_tutorials/pictures/ICELLNET_CAF_barplots.png (43540, 2023-11-20)
exemples_tutorials/pictures/ICELLNET_CAF_networks.png (458109, 2023-11-20)
exemples_tutorials/pictures/ICELLNET_CAF_pvalueplot.png (96038, 2023-11-20)
exemples_tutorials/pictures/ICELLNET_Figure2_V10.png (378239, 2023-11-20)
exemples_tutorials/pictures/ICELLNET_scRNAseq_CHeatmap.png (159409, 2023-11-20)
exemples_tutorials/pictures/ICELLNET_scRNAseq_UMAP.png (204189, 2023-11-20)
exemples_tutorials/pictures/ICELLNET_scRNAseq_barplot.png (91310, 2023-11-20)
exemples_tutorials/pictures/ICELLNET_scRNAseq_heatmap.png (244958, 2023-11-20)
exemples_tutorials/pictures/ICELLNET_scRNAseq_heatmap_spe.png (211643, 2023-11-20)
exemples_tutorials/pictures/ICELLNET_scRNAseq_spe3.png (211578, 2023-11-20)
icellnet/ (0, 2023-11-20)
icellnet/DESCRIPTION (1224, 2023-11-20)
icellnet/NAMESPACE (511, 2023-11-20)
icellnet/R/ (0, 2023-11-20)
icellnet/R/CellPhoneDB_convert.R (4959, 2023-11-20)
icellnet/R/LR.balloon.plot.R (5228, 2023-11-20)
icellnet/R/LR.family.score.R (3232, 2023-11-20)
icellnet/R/LR.heatmap.R (4097, 2023-11-20)
icellnet/R/LR.selection.R (2453, 2023-11-20)
icellnet/R/LR.viz.R (5440, 2023-11-20)
... ...

# Dissection of intercellular communication using the transcriptome-based framework ICELLNET This repository hosts the source code corresponding to the method described in [Nol, 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. --- ## 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 --- ## 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: Nol, 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)

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