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. peaks) searching for motifs (JASPAR by default).

tss_enrichment(data[, features, ...])

Calculate TSS enrichment according to ENCODE guidelines.