Obesity Manuscript analysis

Workflow and Methods

Notebooks replicating the figures in Obesity manuscript

• 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

• ipynb/merge_annotation.ipynb

  • Merge cell type and states annotation:

• ipynb/scCODA.ipynb

  • Cell type propotional test

• ipynb/celltype_general_stats.ipynb

  • Cell type propotional visualization

• ipynb/venn.ipynb

  • draw venn diagram:

• 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

• 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