muon.atac.tl

Functions

add_genes_peaks_groups(data[, ...])	Add gene names to peaks ranked by clustering group
add_peak_annotation(data, annotation[, sep, ...])	Parse peak annotation file and add it to the .uns["atac"]["peak_annotation"]
add_peak_annotation_gene_names(data[, ...])	Add gene names to peak annotation table in .uns["atac"]["peak_annotation"]
count_fragments_features(data[, features, ...])	Count fragments overlapping given Features.
fetch_regions_to_df(fragment_path, features)	Parse peak annotation file and return it as DataFrame.
get_sequences(data, bed, fasta_file[, bed_file])
initialise_default_files(data, path)	Locate default files for ATAC-seq
locate_file(data, key, file)	Add path to the file to .uns["files"][key]
locate_fragments(data, fragments[, ...])	Parse fragments file and add a variable to access it to the .uns["files"]["fragments"]
locate_genome(data, fasta_file)	Add path to the FASTA file with genome to .uns["files"]["genome"]
lsi(data[, scale_embeddings, n_comps])	Run Latent Semantic Indexing
nucleosome_signal(data[, n, ...])	Computes the ratio of nucleosomal cut fragments to nucleosome-free fragments per cell.
rank_peaks_groups(data, groupby[, ...])	Rank peaks in clusters groups.
scan_sequences(sequences[, motif_scanner, ...])	Scan sequences (e.g.
tss_enrichment(data[, features, ...])	Calculate TSS enrichment according to ENCODE guidelines.