Python implementation of emptydrops() in CellRanger v3.0.2
Project 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)
]
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