This repository contains Rmarkdown code, R code and metadata files to build a MetaCell model and generate part of the figures for Cohen et al. Cell 2018 Lung Single-Cell Signaling Interaction Map Reveals Basophil Role in Macrophage Imprinting, Cell 2018
In order to run the Rmd file, downloaded processed data from the GSE119228 needs to be added in specific folders: Processed UMI-tab files (ABXXX.txt) from GSE119228 should be copied to the folder output/umi.tab.
To start analysis, run from the root directory:
R/3.5.0
library(rmarkdown)
rmarkdown::render("scripts/lung_metacell_model.Rmd")
To run ligand receptor analysis run:
rmarkdown::render("scripts/lung_lig_rec.Rmd")
The following R libraries should be installed: data.table, dplyr, graph, methods, Matrix, matrixStats, pheatmap, RColorBrewer, Rgraphviz, KernSmooth, zoo, ggplot2, cluster, cowplot, pdist, doMC, RCurl, igraph, RSvgDevice, dbscan, entropy, parallel, tgconfig, tgutil (>= 0.0.3), tgstat, SingleCellExperiment, BiocManager, gridExtra, reshape2, scales, metacell
install.packages('BiocManager')
BiocManager::install('metacell', site_repository = 'tanaylab.bitbucket.io/repo', update = FALSE)Please send questions to Dikla Gelbard Solodkin or Amir Giladi