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Code for manuscript "Spatially resolved transcriptomics reveals gene signatures underlying the vulnerability of 2 human middle temporal gyrus in Alzheimer's disease"

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01_DEGs of layer specific marker_heatmap.R
01_DEGs of layer specific marker_heatmap.R
 
 
01_DEGs of layer specific markers_vlnplot.R
01_DEGs of layer specific markers_vlnplot.R
 
 
01_Layer specific marker and ab test.R
01_Layer specific marker and ab test.R
 
 
02_DEG of AD v.s. Control in each layer_SCTCPM venn_heatmap.R
02_DEG of AD v.s. Control in each layer_SCTCPM venn_heatmap.R
 
 
02_Umap and spatial plot for integrating objects.R
02_Umap and spatial plot for integrating objects.R
 
 
03_DEG of pathologies v.s. non pathological level_GO analysis for DEGs of each level.R
03_DEG of pathologies v.s. non pathological level_GO analysis for DEGs of each level.R
 
 
04_Fishertest_WGCNA_14 interesting sets.R
04_Fishertest_WGCNA_14 interesting sets.R
 
 
04_WGCNA for variable feature_functional analyses for each module.R
04_WGCNA for variable feature_functional analyses for each module.R
 
 
05_Deconvolution_plot.r
05_Deconvolution_plot.r
 
 
05_Deconvolution_scRNAprocessing.r
05_Deconvolution_scRNAprocessing.r
 
 
05_cell2location_pipeline.py
05_cell2location_pipeline.py
 
 
05_cell2location_run.sh
05_cell2location_run.sh
 
 
06_correlation_SRT_RNAscope_plot.r
06_correlation_SRT_RNAscope_plot.r
 
 
07_specificdeg_logfc.R
07_specificdeg_logfc.R
 
 
README.md
README.md
 
 
Revision_adjustclusternumber.r
Revision_adjustclusternumber.r
 
 
Revision_metainformation_output.r
Revision_metainformation_output.r
 
 
Revision_pathology_deg.r
Revision_pathology_deg.r
 
 
Revision_pathology_significanttest.r
Revision_pathology_significanttest.r
 
 
supplement_DEGs of pathologies.R
supplement_DEGs of pathologies.R
 
 
supplement_GO_countdecimals.R
supplement_GO_countdecimals.R
 
 

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AD-spatial-code

Code for manuscript "Spatially resolved transcriptomics reveals gene signatures underlying the vulnerability of 2 human middle temporal gyrus in Alzheimer's disease"

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Code for manuscript "Spatially resolved transcriptomics reveals gene signatures underlying the vulnerability of 2 human middle temporal gyrus in Alzheimer's disease"

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