API

Classifying Drops

obtain_arrays(data[, path])	Obtain post probabilities of the high and low Gaussian distribution.
classify_drops(base_bv_array, high_array, ...)	Calculate confidence of all GEM cells.
read_full_classify_result(path)	Read classification result from path.
store_full_classify_result(data, ...)	Store the full classification result in {path}/GMM_full.csv.
store_simplified_classify_result(data, ...)	Store the simplified classification result in {path}/GMM_simplified.csv.
purify_droplets(data, confidence_threshold)	Remove empty droplets or with confidence under the threshold.
count_bad_droplets(data, confidence_threshold)	Count empty droplets with or confidence under the threshold.
obtain_SSD_list(data, sample_num[, class_id_ary])	Return GEM barcodes that are SSDs.
obtain_MSM_list(data, sample_num[, idx_list])	Return GEM barcodes that are MSMs.
count_by_class(data, base_bv_array)	Obtain list of count by class.
get_SSD_count_ary(data, SSD_idx, sample_num)	Obtain SSD count list.

Estimating Multiplet rates

compute_relative_SSM_rate(SSM_rate, singlet_rate)	Compute relative SSM rate over singlet rate.
compute_SSM_rate_with_cell_num(cell_num, ...)	Compute SSM rate with cell numbers.
compute_SSD_num(drop_num, subject_cell_num, ...)	Compute SSM rate with cell numbers.
phony_cluster_MSM_rate(cell_num_ary[, ...])	Estimate phony cluster MSM rate with cell numbers.
get_tau_cell_num(drop_num, total_cell_num, ...)	Get tau cell number.
pure_cluster_MSM_rate(drop_num, ...[, ...])	Estimate pure cluster MSM rate.
test_phony_hypothesis(cluster_MSM_num, ...)	Test phony-type hypothesis.
test_pure_hypothesis(cluster_MSM_num, ...[, ...])	Test pure-type hypothesis.

Computing Tools

obtain_base_bv_array(sample_num)	Returns the binary array representing all combinations of cells.
check_set_bit(bv, bit_pos)	Return true if the bit_pos th bit of bv is 1.
init_mask(sample_num)	Return an empty BitVector.BitVector object of sample_num size.
set_bit(bv, bit_pos)	Set the bit_pos th bit of bv as 1.
gather_multiplet_rates(venn_values, ...)	Compute MSM/SSM/Singlet rates.
obtain_HTO_GEM_num(data, base_bv_array)	Find HTO numbers from the given data.
param_scaling(params, scaler, operator)	Get parameters for estimation.
compute_scaler(params)	Compute scaler for parameters.
obtain_experiment_params(base_bv_array, ...)	Get parameters for estimation.