README.md

Mouse-Diabetic-Kidney-Disease-Single-Cell-Atlas

This repository documented the scripts to generate the data for our manuscript entitled Mapping the Single Cell Transcriptomic Response of Murine Diabetic Kidney Disease to Therapies.
The raw and processed data have been deposited on Gene Expression Omnibus (GSE184652). A searchable database, including gene expression in all kidney cell types, glomerular cell types, and PCT cell types is available at our Kidney Interactive Transcriptomics (K.I.T.) website: http://humphreyslab.com/SingleCell/.

Descriptions

1. Scripts for Figure 2

data_processing/
clustering/
plot_figures/figure2.R

2. Scripts for Figure 3

Differential_gene_analysis/
MAGMA_analysis/
plot_figures/figure3.R

3. Scripts for Figure 4

Differential_gene_analysis/
Cell-Cell_interaction_analysis/
Pathway_analysis/
plot_figures/figure4.R

4. Scripts for Figure 5

Differential_gene_analysis/
pySCENIC_analysis/
plot_figures/figure5.R

5. Scripts for Figure 6

clustering/
Bulk_RNAseq_analysis/
Deconvolution_analysis/
Cell-Cell_interaction_analysis/
plot_figures/figure6.R

6. Scripts for Figure 7

Differential_gene_analysis/
Pathway_analysis/
plot_figures/figure7.R

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