Notebooks and scripts for epicardioids analysis

• notebooks

  • analyse_signac_unfiltered.ipynb: QC filtering of ATAC data
  • cellrank_analysis.ipynb: CellRank analysis on metacells
  • create_anndata.ipynb: Loading of raw data into anndata
  • epicardial_subclustering.ipynb: Analysis for epicardial cells
  • epicardioids_metacell_analysis.ipynb : Analysis of metacells, clustering, DEG
  • impute_weights_magic.ipynb : Gene activity imputation on metacell embedding
  • jcf_subclustering.ipynb: Analysis for JCF cells
  • pando_grn.ipynb : Pando GRN inference on JCF cells
  • scglue_unfiltered.ipynb : scGLUE to generate metacell embeddings (this needs bipartite matching)
  • scvelo_analysis.ipynb: scvelo analysis on RNA modality

• scripts

  • amulet: Doublet detection using Amulet
  • integration: Bipartite matching (matching ATAC to RNA cells) on scGLUE embedding