The code is used for reproduce for publicatioin: XXXX
scRNA-seq data analysis
Generally, it can divided into following steps:
- merge 14 samples into a matrix file
python step1_merge_data.py
- preprocess the matrix
python step2_preprocess.py
- extract samples (remove samples with low quality) and bbknn
python step3_extract_samples.py
python step3_merge_bbknn.py #bbknn
- cell population clustering (cell type level)
python step4_populations.py
- CAF subpopulation clustering (sub cell type level)
python step5_subpopulation.py
- scripts used for visualization the single cell data
python step6_plot_genes_umap.py
python step6_plot_umap_sample.py
python step6_plot_genes_dotplot_conditions.py
paga analysis
python do_paga.py
spatial analysis part
python spatial.py
enrichment analysis
python run_over_representation_analysis_sc_csv.py
python prerank_test.py
conda enviroment
details in packages_in_conda.txt