API

Preprocessing

get_bg_peaks(data[, niterations, n_jobs])	Find background peaks based on GC bias and number of reads per peak
add_peak_seq(data, genome_file[, delimiter])	Add the DNA sequence of each peak to data object.
add_gc_bias(data)	Compute GC bias for each peak.

Motif match

match_motif(data, motifs[, pseudocounts, ...])

Perform motif matching to predict binding sites using MOODS.

Genome

get_genome([genome, output_dir])

Download genome

Compute deviation

compute_deviations(data[, n_jobs])	Compute raw and bias-corrected deviations.
compute_expectation(count)	Compute expetation accessibility per peak and per cell by assuming identical read probability per peak for each cell with a sequencing depth matched to that cell observed sequencing depth