Add Topyfic snakemake - Githubissues

EngreitzLab / gene_network_evaluation

Evaluation framework for computationally inferred gene networks from single-cell data.

GNU General Public License v2.0

9 stars 7 forks source link

Add Topyfic snakemake #30

Closed nargesr closed 2 months ago

nargesr commented 2 months ago

I kept the previous version in a directory called 'V0' for now. Since we decided to keep the evaluation pipeline and gene program interfaces separate, the snakemake would only run the Topyfic. We also need a small script to convert Topyfic outputs to something compatible with the evaluation pipeline. This can be added at the end of the Topyfic snakemake as well. We should talk about this in our upcoming meeting this week.

adamklie commented 2 months ago

Keep all of the program keys in single MuData

Example data: https://www.synapse.org/Synapse:syn61874907

MuData object with n_obs × n_vars = 92284 × 5551
2 modalities
rna:    92284 x 5451
  obs:  'sample', 'species', 'gene_count', 'tscp_count', 'mread_count', 'leiden', 'n_counts'
  obsm: 'X_pca', 'X_umap'
  layers:   'norm10k'
factor_analysis_K100:   92284 x 100
  obs:  'sample', 'species', 'gene_count', 'tscp_count', 'mread_count', 'leiden', 'n_counts'
  uns:  'loadings_genes'
  varm: 'loadings'