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README.md
README.md
 
 
clinical_pie.R
clinical_pie.R
 
 
code_for_Enterotype_identification.ipynb
code_for_Enterotype_identification.ipynb
 
 
draw_metag_data_collect_worldmap.R
draw_metag_data_collect_worldmap.R
 
 
metaForest.R
metaForest.R
 
 
s01.draw_kmeans_clusters.R
s01.draw_kmeans_clusters.R
 
 
s01_merge_signatures.py
s01_merge_signatures.py
 
 
s08_aging_atb_response.R
s08_aging_atb_response.R
 
 
s09_enterotype_DA_species_shown.R
s09_enterotype_DA_species_shown.R
 
 
s10_nsclc_RNAseq_GSEA.R
s10_nsclc_RNAseq_GSEA.R
 
 
step1.mergeData.R
step1.mergeData.R
 
 
step2.1.qc_scaledata.R
step2.1.qc_scaledata.R
 
 
step2.4.doublet.scrublet.python.ipynb
step2.4.doublet.scrublet.python.ipynb
 
 
step2.5.2.filter_junk_conertSeuratTOh5ad.ipynb
step2.5.2.filter_junk_conertSeuratTOh5ad.ipynb
 
 
step2.5.3.filter_junk_scanpy_pipeline.01_drawAgain.py
step2.5.3.filter_junk_scanpy_pipeline.01_drawAgain.py
 
 
step2.5.3.filter_junk_scanpy_pipeline.02_drawAgain.R
step2.5.3.filter_junk_scanpy_pipeline.02_drawAgain.R
 
 
step2.5.3.filter_junk_scanpy_pipeline.ipynb
step2.5.3.filter_junk_scanpy_pipeline.ipynb
 
 
step2.5.3.filter_junk_scanpy_pipeline_subset_Tcells_v2.R
step2.5.3.filter_junk_scanpy_pipeline_subset_Tcells_v2.R
 
 
step2.5.3.filter_junk_scanpy_pipeline_subset_Tcells_v2.py
step2.5.3.filter_junk_scanpy_pipeline_subset_Tcells_v2.py
 
 
step2.5.4.filter_junk_scanpy_pipeline_merge_obsdata.ipynb.v2.R
step2.5.4.filter_junk_scanpy_pipeline_merge_obsdata.ipynb.v2.R
 
 
step6_merge_adataobs.R
step6_merge_adataobs.R
 
 
step6_merge_adataobs.py
step6_merge_adataobs.py
 
 

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scRNA_Aging_TME

this is the code script used for data analysis in the manuscript "A specific enterotype derived from gut microbiome of the elderly enables favorable responses to immune checkpoint blockade therapy" by Xiaoqiang Zhu et al.

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