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| genomeIntervals-package | Operations on genomic intervals |
| $-method | Class "Genome\_intervals" |
| $<--method | Class "Genome\_intervals" |
| .readGff3 | readGff3 |
| annotation | Class "Genome\_intervals" |
| annotation-method | Class "Genome\_intervals" |
| annotation<- | Class "Genome\_intervals" |
| annotation<--method | Class "Genome\_intervals" |
| as | Coercion methods of the genomeIntervals package |
| as-method | Coercion methods of the genomeIntervals package |
| c | c extension for the 'genomeIntervals package' |
| c-method | c extension for the 'genomeIntervals package' |
| coerce-method | Class "Genome\_intervals" |
| coerce-method | Coercion methods of the genomeIntervals package |
| coerce-method | Class "Genome\_intervals\_stranded" |
| core_annotated | Genome intervals with minimal annotation |
| core_annotated-method | Genome intervals with minimal annotation |
| distance_to_nearest | Distance in bases to the closest interval(s) |
| distance_to_nearest-method | Distance in bases to the closest interval(s) |
| GenomeIntervals | Constructor function for genomeIntervals objects |
| genomeIntervals | Operations on genomic intervals |
| genomeIntervals coercion methods | Coercion methods of the genomeIntervals package |
| GenomeIntervals-constructor | Constructor function for genomeIntervals objects |
| Genome_intervals deprecated functions | The following function have been deprecated: • 'seq_name' • 'seq_name<-' |
| Genome_intervals-class | Class "Genome\_intervals" |
| Genome_intervals-ordering | Ordering methods for Genome intervals |
| Genome_intervals_stranded-class | Class "Genome\_intervals\_stranded" |
| gen_ints | Genome Intervals examples |
| getGffAttribute | Pull one or more key/value pairs from gffAttributes strings |
| i | Genome Intervals examples |
| interval_complement | Genome interval set operations |
| interval_complement-method | Genome interval set operations |
| interval_intersection | Genome interval set operations |
| interval_intersection-method | Genome interval set operations |
| interval_overlap | Assess overlap from one set of genomic intervals to another |
| interval_overlap-method | Assess overlap from one set of genomic intervals to another |
| interval_union | Genome interval set operations |
| interval_union-method | Genome interval set operations |
| inter_base | Class "Genome\_intervals" |
| inter_base-method | Class "Genome\_intervals" |
| inter_base<- | Class "Genome\_intervals" |
| inter_base<--method | Class "Genome\_intervals" |
| j | Genome Intervals examples |
| k | Genome Intervals examples |
| order | Ordering methods for Genome intervals |
| order-method | Ordering methods for Genome intervals |
| parseGffAttributes | Parse out the gffAttributes column of a Genome\_intervals object |
| rank | Ordering methods for Genome intervals |
| rank-method | Ordering methods for Genome intervals |
| readBasePairFeaturesGff3 | readGff3 |
| readBasePairFeaturesGff3-method | readGff3 |
| readGff3 | readGff3 |
| readGff3-method | readGff3 |
| readZeroLengthFeaturesGff3 | readGff3 |
| readZeroLengthFeaturesGff3-method | readGff3 |
| seqnames-method | Class "Genome\_intervals" |
| seqnames<--method | Class "Genome\_intervals" |
| seq_name | The following function have been deprecated: • 'seq_name' • 'seq_name<-' |
| seq_name-method | The following function have been deprecated: • 'seq_name' • 'seq_name<-' |
| seq_name<- | The following function have been deprecated: • 'seq_name' • 'seq_name<-' |
| seq_name<--method | The following function have been deprecated: • 'seq_name' • 'seq_name<-' |
| show-method | Class "Genome\_intervals" |
| size-method | Class "Genome\_intervals" |
| sort | Ordering methods for Genome intervals |
| sort-method | Ordering methods for Genome intervals |
| strand | Class "Genome\_intervals\_stranded" |
| strand-method | Class "Genome\_intervals\_stranded" |
| strand<- | Class "Genome\_intervals\_stranded" |
| strand<--method | Class "Genome\_intervals" |
| strand<--method | Class "Genome\_intervals\_stranded" |
| type<--method | Class "Genome\_intervals" |
| which_nearest-method | Class "Genome\_intervals" |
| width-method | Class "Genome\_intervals" |
| writeGff3 | readGff3 |
| writeGff3-method | readGff3 |
| xtfrm | Ordering methods for Genome intervals |
| xtfrm-method | Ordering methods for Genome intervals |
| [-method | Class "Genome\_intervals" |
| [<--method | Class "Genome\_intervals" |
| [[-method | Class "Genome\_intervals" |
| [[<--method | Class "Genome\_intervals" |