Metadata-Version: 2.1
Name: emptydrops
Version: 0.0.5
Summary: Python implementation of emptydrops() in CellRanger v3.0.2
Home-page: https://github.com/nh3/emptydrops
Author: nh3
Author-email: nh3@users.noreply.github.com
License: UNKNOWN
Description: # emptydrops
        Python implementation of emptydrops-like cell calling as in CellRanger v3.0.2
        
        ## Disclaimer:
        All code originally comes from https://github.com/10XGenomics/cellranger with
        minimal modifications for packaging and running under python3.
        
        ## Usage:
        ```
        from emptydrops import find_nonambient_barcodes
        from emptydrops.matrix import CountMatrix
        
        matrix = CountMatrix.from_legacy_mtx(mtx_dir)
        
        find_nonambient_barcodes(
            matrix,          # Full expression matrix
            orig_cell_bcs,   # (iterable of str): Strings of initially-called cell barcodes
            min_umi_frac_of_median=0.01,
            min_umis_nonambient=500,
            max_adj_pvalue=0.01
        )
        ```
        
        Returns:
        ```
        [
            'eval_bcs',      # Candidate barcode indices in addition to those in `orig_cell_bcs` (n)
            'log_likelihood',# Ambient log likelihoods (n)
            'pvalues',       # pvalues (n)
            'pvalues_adj',   # B-H adjusted pvalues (n)
            'is_nonambient', # Boolean nonambient calls (n)
        ]
        ```
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Description-Content-Type: text/markdown
