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CheckAtlas

note

A one-liner tool for quality control of your single-cell atlases.

https://github.com/becavin-lab/checkatlas

CheckAtlas is a one-liner tool to check the quality of your single-cell atlases. For every atlas, it produces quality control tables and figures which can then be processed by MultiQC. CheckAtlas is able to load Scanpy, Seurat, and CellRanger files.

MultiQC parses the following tables produced by CheckAtlas:

  • summary/sample_name.tsv - Summary tables with general information on atlases
  • adata/sample_name.tsv - Table with all scanpy adata features
  • qc/sample_name.tsv - Quality control tables for every atlas
  • cluster/sample_name.tsv - Table with cluster metrics calculated for every atlas
  • annot/sample_name.tsv - Table with annotation metrics calculated for every atlas
  • dimred/sample_name.tsv - Table with dimensionality reduction metrics calculated for every atlas

File search patterns​

checkatlas/adata:
  contents_re: ^atlas_obs\tobsm\tvar\tvarm\tuns
  fn: '*.tsv'
  num_lines: 1
checkatlas/annotation:
  contents_re: ^Annot_Sample\tReference\tobs
  fn: '*.tsv'
  num_lines: 1
checkatlas/cluster:
  contents_re: ^Clust_Sample\tobs
  fn: '*.tsv'
  num_lines: 1
checkatlas/dimred:
  contents_re: ^Dimred_Sample\tobsm
  fn: '*.tsv'
  num_lines: 1
checkatlas/qc:
  contents_re: cellrank_(total_counts|n_genes_by_counts|pct_counts_mt)
  fn: '*.tsv'
  num_lines: 1
checkatlas/summary:
  contents_re: ^AtlasFileType\tNbCells\tNbGenes
  fn: '*.tsv'
  num_lines: 1
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