Home

Welcome to the DIALOGUE!

DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to identify multicellular programs (MCPs) and map the cell transcriptome as a function of its environment. Given single-cell data, it combines penalized matrix decomposition with multilevel modeling to identify generalizable MCPs and examines their association with specific phenotypes of interest.

Requirements

• R (tested in R version 3.4.0).
• R libraries: lme4, lmerTest, PMA, plyr, matrixStats, psych, stringi, RColorBrewer, unikn, reshape2, ggplot2

Quick start

To install you can either use devtools::install_github("DIALOGUE",your_user_name) or just download tha package and use devtools::install("DIALOGUE")

Here you can find simple step-by-step examples on existing data and new data.

In a nutshell, the input will include the single-cell transcriptomes of different cell types, usually together with some more compact representation (e.g., PCs). The output will be multicellular programs (MCPs) of co-regulated genes across the different cell types. Each MCP consists of cell-type-specific gene subsets. For more specific cell-cell "interactions" you can run the pairwise version, using the data of two cell types of interest as input. DIALOGUE can also identify MCPs that span more multiple cell types (see Jerby-Arnon and Regev BioRxiv 2020 for examples on 5 and 6 cell types).

Citation

Jerby-Arnon and Regev Mapping multicellular programs from single-cell transcriptomes.