gcell.rna.gencode.Gencode

class gcell.rna.gencode.Gencode(assembly='hg38', version=None, is_basic=True, exclude_chrs=['chrM', 'chrY'])

A class to handle GENCODE gene annotations for different genome assemblies.

GENCODE (https://www.gencodegenes.org/) provides high-quality gene annotations for human and mouse genomes. This class handles downloading, parsing, and accessing GENCODE annotation data.

The class inherits from GTF and provides convenient methods to access gene information like strand, chromosome location, transcription start sites, etc.

Attributes

DEFAULT_VERSIONS
gene_to_chrom	Dict mapping gene names to their chromosome locations.
gene_to_id	Dict mapping gene names to their GENCODE IDs.
gene_to_strand	Dict mapping gene names to their strand orientation ('+' or '-').
gene_to_strand_numeric	Dict mapping gene names to numeric strand values (0 for '+', 1 for '-').
gene_to_tes	Dict mapping gene names to their transcription end sites (TES).
gene_to_tss	Dict mapping gene names to their transcription start sites (TSS).
gene_to_type	Dict mapping gene names to their gene types (e.g., protein_coding, lincRNA).
id_to_gene	Dict mapping GENCODE IDs to gene names.
original_gtf

Methods

from_config(config)	Create a Gencode instance from a configuration dictionary.
get_exp_feather(peaks[, extend_bp])	Get the expression data for the given peaks.
get_gene(gene_name)	Get a Gene object for the given gene name.
get_gene_id(gene_id)	Get a Gene object for the given gene ID.
get_genebodies([gene_names])	Get the gene bodies for the given gene names.
get_genes(gene_names)	Get a list of Gene objects for the given gene names.
query_region(chrom, start, end[, strand])	Query the GTF for regions matching the given parameters.