Preprocessing

Note

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Preprocessing

Filtering using preprocessing.filter_guide_reads()

filter_guide_reads(gem_path, guide_prefix=None, output_path=None, binarilize=False, assign_pattern='max', filter_threshold=None)

Filter and process guide reads from a GEM file.

Parameters:

• gem_path – Path to the input GEM file

• guide_prefix – Optional prefix to filter guide names. Only guides starting with this prefix will be kept

• output_path – Optional path to save filtered results. If None, returns the filtered DataFrame

• binarilize – Whether to set all bin counts to 1. Recommended for high library size and resolution

• assign_pattern – How to handle bins with multiple guides. Can be ‘max’ (keep guide with max count), ‘drop’ (remove multi-guide bins), or ‘all’ (keep all guides)

• filter_threshold – Minimum guide count threshold. Bins with guides below this count will be filtered out

Returns:

Filtered pandas DataFrame if output_path is None, otherwise None