API of GenomKit

• Genomic Sequences
  • GSequence
    • GSequence.complement()
    • GSequence.count_table()
    • GSequence.dna2rna()
    • GSequence.reverse()
    • GSequence.reverse_complement()
    • GSequence.rna2dna()
    • GSequence.slice_sequence()
    • GSequence.trim()
  • GSequences
    • GSequences.add()
    • GSequences.complement()
    • GSequences.count_table()
    • GSequences.dna2rna()
    • GSequences.get_sequence()
    • GSequences.load()
    • GSequences.reverse()
    • GSequences.reverse_complement()
    • GSequences.rna2dna()
    • GSequences.trim()
• Genomic Alignments
  • GAlignments
    • GAlignments.calculate_coverage()
    • GAlignments.load_reads()
• Genomic Regions
  • GRegion
    • GRegion.bed_entry()
    • GRegion.distance()
    • GRegion.extend()
    • GRegion.extend_fold()
    • GRegion.overlap()
    • GRegion.resize()
  • GRegions
    • GRegions.add()
    • GRegions.close_regions()
    • GRegions.cluster()
    • GRegions.extend()
    • GRegions.extend_fold()
    • GRegions.filter_by_names()
    • GRegions.filter_by_score()
    • GRegions.get_GSequences()
    • GRegions.get_names()
    • GRegions.get_sequences()
    • GRegions.intersect()
    • GRegions.load()
    • GRegions.merge()
    • GRegions.remove_duplicates()
    • GRegions.resize()
    • GRegions.sampling()
    • GRegions.sort()
    • GRegions.split()
    • GRegions.subtract()
    • GRegions.total_coverage()
    • GRegions.write()
  • GRegionsSet
    • GRegionsSet.add()
    • GRegionsSet.combine()
    • GRegionsSet.count_overlaps()
    • GRegionsSet.get_lengths()
    • GRegionsSet.get_names()
    • GRegionsSet.load_pattern()
    • GRegionsSet.subtract()
• Genomic Annotation
  • GAnnotation
    • GAnnotation.filter_elements()
    • GAnnotation.get_exon()
    • GAnnotation.get_exon_ids()
    • GAnnotation.get_gene()
    • GAnnotation.get_gene_ids()
    • GAnnotation.get_gene_names()
    • GAnnotation.get_regions()
    • GAnnotation.get_transcript()
    • GAnnotation.get_transcript_ids()
    • GAnnotation.load_data()
• Genomic Coverages
  • GCoverages
    • GCoverages.calculate_coverage_GRegions()
    • GCoverages.calculate_coverage_GRegions2()
    • GCoverages.calculate_coverage_from_bam()
    • GCoverages.filter_regions_coverage()
    • GCoverages.flip_negative_regions()
    • GCoverages.get_coverage()
    • GCoverages.get_dataframe()
    • GCoverages.load_coverage_from_bigwig()
    • GCoverages.scale_coverage()
    • GCoverages.total_sequencing_depth()
• Genomic Variants
  • GVariants
    • GVariants.load()
    • GVariants.to_GRegions()