ccb-sb/2023_mouse_ear_non-thermal_plasma

Skin treatment with non-thermal plasma modulates the immune system through miR-223-3p and its target genes

This repository contains the code necessary to produce the publication figures via a snakemake workflow.

Necessary files

Provide the following files in the appropriate directories.

name	source	target path
raw counts	GEO Series GSE236788 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE236788)	data/expression/raw/GSE236788_miRNA_expression_raw.tsv
KEGG	miRPathDB v2.0 (https://mpd.bioinf.uni-sb.de/download/version_2/miRPathDB2_mmu_p_values.tar.gz)	data/external_data/mirpathd/KEGG_prediction_union.csv
human cellular microRNAome database	Supplementary tables (https://doi.org/10.1093/gigascience/giac083)	data/external_data/giac083_supplemental_files/Supplementary_Table_S2.xlsx data/external_data/giac083_supplemental_files/Supplementary_Table_S7.xlsx

Running the pipeline

# run snakemake in this folder
snakemake
# use conda a backend if mamba is not available
snakemake --use-conda --conda-frontend conda

Results

If the pipeline suceeded, results are availabe in the publication folder. The names are according to the figures in the publication whereas fig_2b_1 corresponds to the top left plot of Fig. 2b.

License

MIT © CCB-SB