scgenome.tl.count_gc

scgenome.tl.count_gc(bins, genome_fasta, column_name='gc', proportion=False)

Count gc in each bin

Parameters:

• bins (pyranges.PyRanges) – ranges for which to count gc

• genome_fasta (str) – reference genome fasta

• column_name (str, optional) – column to add to bins, by default ‘gc’

• proportion (bool, optional) – proportion of length, by default False

Returns:

output ranges with additional column for gc count

Return type:

pyranges.PyRanges