Index

A

add() (genomkit.coverages.gcoverages_set.GCoveragesSet method) (genomkit.regions.gregions.GRegions method) (genomkit.regions.gregions_set.GRegionsSet method) (genomkit.sequences.gsequences.GSequences method)

B

bed_entry() (genomkit.regions.gregion.GRegion method)

C

calculate_coverage() (genomkit.alignments.galignments.GAlignments method) calculate_coverage_from_bam() (genomkit.coverages.gcoverages.GCoverages method) calculate_coverage_GRegions() (genomkit.coverages.gcoverages.GCoverages method) calculate_coverage_GRegions2() (genomkit.coverages.gcoverages.GCoverages method) close_regions() (genomkit.regions.gregions.GRegions method) cluster() (genomkit.regions.gregions.GRegions method)

combine() (genomkit.regions.gregions_set.GRegionsSet method) complement() (genomkit.sequences.gsequence.GSequence method) (genomkit.sequences.gsequences.GSequences method) count_overlaps() (genomkit.regions.gregions_set.GRegionsSet method) count_table() (genomkit.sequences.gsequence.GSequence method) (genomkit.sequences.gsequences.GSequences method)

D

distance() (genomkit.regions.gregion.GRegion method)

dna2rna() (genomkit.sequences.gsequence.GSequence method) (genomkit.sequences.gsequences.GSequences method)

E

extend() (genomkit.regions.gregion.GRegion method) (genomkit.regions.gregions.GRegions method)

extend_fold() (genomkit.regions.gregion.GRegion method) (genomkit.regions.gregions.GRegions method) extract_seqs_by_regions() (genomkit.sequences.gsequences.GSequences method)

F

filter_by_names() (genomkit.regions.gregions.GRegions method) filter_by_score() (genomkit.regions.gregions.GRegions method) filter_elements() (genomkit.annotation.gannotation.GAnnotation method)

filter_regions_coverage() (genomkit.coverages.gcoverages.GCoverages method) flip_negative_regions() (genomkit.coverages.gcoverages.GCoverages method) (genomkit.coverages.gcoverages_set.GCoveragesSet method)

G

GAlignments (class in genomkit.alignments.galignments) GAnnotation (class in genomkit.annotation.gannotation) GCoverages (class in genomkit.coverages.gcoverages) GCoveragesSet (class in genomkit.coverages.gcoverages_set) genomkit.alignments module genomkit.alignments.galignments module genomkit.annotation module genomkit.annotation.gannotation module genomkit.coverages module genomkit.coverages.gcoverages module genomkit.coverages.gcoverages_set module genomkit.regions module genomkit.regions.gregion module genomkit.regions.gregions module genomkit.regions.gregions_set module genomkit.sequences module genomkit.sequences.gsequence module

genomkit.sequences.gsequences module genomkit.variants module genomkit.variants.gvariant module genomkit.variants.gvariants module get_coverage() (genomkit.coverages.gcoverages.GCoverages method) get_dataframe() (genomkit.coverages.gcoverages.GCoverages method) get_exon() (genomkit.annotation.gannotation.GAnnotation method) get_exon_ids() (genomkit.annotation.gannotation.GAnnotation method) get_gene() (genomkit.annotation.gannotation.GAnnotation method) get_gene_ids() (genomkit.annotation.gannotation.GAnnotation method) get_gene_names() (genomkit.annotation.gannotation.GAnnotation method) get_GSequences() (genomkit.regions.gregions.GRegions method) get_lengths() (genomkit.regions.gregions_set.GRegionsSet method) get_names() (genomkit.coverages.gcoverages_set.GCoveragesSet method) (genomkit.regions.gregions.GRegions method) (genomkit.regions.gregions_set.GRegionsSet method) get_regions() (genomkit.annotation.gannotation.GAnnotation method) get_sequence() (genomkit.sequences.gsequences.GSequences method) get_sequences() (genomkit.regions.gregions.GRegions method) get_transcript() (genomkit.annotation.gannotation.GAnnotation method) get_transcript_ids() (genomkit.annotation.gannotation.GAnnotation method) GRegion (class in genomkit.regions.gregion) GRegions (class in genomkit.regions.gregions) GRegionsSet (class in genomkit.regions.gregions_set) GSequence (class in genomkit.sequences.gsequence) GSequences (class in genomkit.sequences.gsequences) GVariants (class in genomkit.variants.gvariants)

I

intersect() (genomkit.regions.gregions.GRegions method)

L

load() (genomkit.regions.gregions.GRegions method) (genomkit.sequences.gsequences.GSequences method) (genomkit.variants.gvariants.GVariants method)

load_coverage_from_bigwig() (genomkit.coverages.gcoverages.GCoverages method) load_data() (genomkit.annotation.gannotation.GAnnotation method) load_pattern() (genomkit.regions.gregions_set.GRegionsSet method) load_reads() (genomkit.alignments.galignments.GAlignments method)

M

merge() (genomkit.regions.gregions.GRegions method) module genomkit.alignments genomkit.alignments.galignments genomkit.annotation genomkit.annotation.gannotation genomkit.coverages genomkit.coverages.gcoverages genomkit.coverages.gcoverages_set genomkit.regions genomkit.regions.gregion genomkit.regions.gregions genomkit.regions.gregions_set genomkit.sequences genomkit.sequences.gsequence genomkit.sequences.gsequences genomkit.variants genomkit.variants.gvariant genomkit.variants.gvariants

O

overlap() (genomkit.regions.gregion.GRegion method)

R

remove_by_names() (genomkit.regions.gregions.GRegions method) remove_duplicates() (genomkit.regions.gregions.GRegions method) resize() (genomkit.regions.gregion.GRegion method) (genomkit.regions.gregions.GRegions method) reverse() (genomkit.sequences.gsequence.GSequence method) (genomkit.sequences.gsequences.GSequences method)

reverse_complement() (genomkit.sequences.gsequence.GSequence method) (genomkit.sequences.gsequences.GSequences method) rna2dna() (genomkit.sequences.gsequence.GSequence method) (genomkit.sequences.gsequences.GSequences method)

S

sampling() (genomkit.regions.gregions.GRegions method) scale_coverage() (genomkit.coverages.gcoverages.GCoverages method) slice_sequence() (genomkit.sequences.gsequence.GSequence method)

sort() (genomkit.regions.gregions.GRegions method) split() (genomkit.regions.gregions.GRegions method) subtract() (genomkit.regions.gregions.GRegions method) (genomkit.regions.gregions_set.GRegionsSet method)

T

to_GRegions() (genomkit.variants.gvariants.GVariants method) total_coverage() (genomkit.regions.gregions.GRegions method)

total_sequencing_depth() (genomkit.coverages.gcoverages.GCoverages method) trim() (genomkit.sequences.gsequence.GSequence method) (genomkit.sequences.gsequences.GSequences method)

W

write() (genomkit.regions.gregions.GRegions method)