get_intercell_networks: Get the cancer-specific intercellular networks, including a...

In olapuentesantana/easierData: easier internal data and exemplary dataset from IMvigor210CoreBiologies package

Description

Obtain the cancer-specific intercellular networks based on literature supported pairs from the Ramilowski database (Ramilowski et al., Nat.Commun., 2015), filtering for 24 cell types acknowledged to be present in the TME. Additionally, a pan-cancer cell type is included using data from the CCLE (Barretina et al., Nature, 2012) by computing the median expression of each gene across cell lines related to the selected cancer types. A pan-cancer network is also available and this is based on the union of all ligand-receptor pairs present across the cancer-specific networks.

Usage

get_intercell_networks()

Value

A list containing for each cancer type, a data.frame with cell-cell ligands and receptors information.

References

Ramilowski, Jordan A., Tatyana Goldberg, Jayson Harshbarger, Edda Kloppmann, Marina Lizio, Venkata P. Satagopam, Masayoshi Itoh, et al. 2015. “A Draft Network of Ligand–Receptor-Mediated Multicellular Signalling in Human.” Nature Communications 6 (1): 7866. https://doi.org/10.1038/ncomms8866.

Barretina, J., Caponigro, G., Stransky, N. et al. The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature 483, 603–607 (2012). https://doi.org/10.1038/nature11003

Examples

if (interactive()) {
    intercell_networks <- get_intercell_networks()
}

olapuentesantana/easierData documentation built on Dec. 22, 2021, 4:19 a.m.