Preprocessing¶
Functions for preprocessing of single cell RNA-seq counts
- palantir.preprocess.filter_counts_data(data, cell_min_molecules=1000, genes_min_cells=10)View on GitHub¶
Remove low molecule count cells and low detection genes
- Parameters:
data – Counts matrix: Cells x Genes
cell_min_molecules – Minimum number of molecules per cell
genes_min_cells – Minimum number of cells in which a gene is detected
- Returns:
Filtered counts matrix
- palantir.preprocess.log_transform(data, pseudo_count=0.1)View on GitHub¶
Log transform the matrix
- Parameters:
data – Counts matrix: Cells x Genes or Anndata object
- Returns:
Log transformed matrix
- palantir.preprocess.normalize_counts(data)View on GitHub¶
Correct the counts for molecule count variability
- Parameters:
data – Counts matrix: Cells x Genes
- Returns:
Normalized matrix