This package provides functions to run differentiable loop extrusion model on HiC/Micro-C experiments formated as mcool files.

Usage:

DLEM [-h] [--stride STRIDE] [--window-size WINDOW_SIZE] [--model-name MODEL_NAME] [--chrom-subset CHROM_SUBSET [CHROM_SUBSET ...]]
            [--perc-nan-threshold PERC_NAN_THRESHOLD] [--lr LR] [--reader-name READER_NAME]
            cooler_file output_path resolution

• cooler_file: Specifies path to the mcool file.
• output_path: Specifies path to the TSV file.
• resolution: Specifies the resolution of the contact map. The corresponding map should exist in mcool.
• WINDOW_SIZE: Algorithm fits patches along the diagonal of the contact map. This specifies the dimensions of the square patch. The default is 2MB/resolution.
• MODEL_NAME: Specifies a model other than the default DLEM model to fit to the data. See models under dlem/models.
• CHROM_SUBSET: If given the model only fits the contact map from these chromosomes.
• PERC_NAN_THRESHOLD: If the percentage of the missing positions in the patch exceeds this threshold the patch is skipped.
• LR: learning rate for the model fit. ADAM is used.
• READER_NAME: Default reader reads from mcool files and returns an array. The user can provide different readers to read from different file types. See the readers under dlem/readers.