-
ipynb/process_10x-cellbender.ipynb
- pre-process and cluster:
-
ipynb/marker_dotplots.ipynb
- cell type markers dot plot
-
ipynb/stb_recluster.py
- Syncytialtrophoblast states, downstream analysis and visualization
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ipynb/merge_annotation.ipynb
- Merge cell type and states annotation:
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ipynb/scCODA.ipynb
- Cell type propotional test
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ipynb/celltype_general_stats.ipynb
- Cell type propotional visualization
-
ipynb/venn.ipynb
- draw venn diagram:
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ipynb/score_lineplot.ipynb
- C-score line plot
-
ipynb/decouple_bp_hallmark.ipynb
- GSEA analysis
- Rmd/adjust_gsea.Rmd: adjust p-values by BH method
-
ipynb/dotplots pathway genes.ipynb
- Dotplots of the genes involved in given pathways
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ipynb/pie.ipynb
- Pie plots
-
ipynb/de_liana.ipynb
- generate the adjency matrix
- ipynb/network_rl.ipynb: network analysis
-
Rmd/Primeseq/*
- downstream analysis of Primeseq data from trophoblast organoids
- Rmd/intersect_TO_tissue.Rmd: intersect of all sets
-
ipynb/venn.ipynb
- Venn: draw venn diagram