Index

A

add() (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)

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)

G

GAlignments (class in genomkit.alignments.galignments) GAnnotation (class in genomkit.annotation.gannotation) GCoverages (class in genomkit.coverages.gcoverages) genomkit.alignments module genomkit.alignments.galignments module genomkit.annotation module genomkit.annotation.gannotation module genomkit.coverages module genomkit.coverages.gcoverages 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.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.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_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)