Package: genomeIntervals 1.63.0
Julien Gagneur
genomeIntervals: Operations on genomic intervals
This package defines classes for representing genomic intervals and provides functions and methods for working with these. Note: The package provides the basic infrastructure for and is enhanced by the package 'girafe'.
Authors:
genomeIntervals_1.63.0.tar.gz
genomeIntervals_1.63.0.zip(r-4.5)genomeIntervals_1.63.0.zip(r-4.4)genomeIntervals_1.63.0.zip(r-4.3)
genomeIntervals_1.63.0.tgz(r-4.4-any)genomeIntervals_1.63.0.tgz(r-4.3-any)
genomeIntervals_1.63.0.tar.gz(r-4.5-noble)genomeIntervals_1.63.0.tar.gz(r-4.4-noble)
genomeIntervals_1.63.0.tgz(r-4.4-emscripten)genomeIntervals_1.63.0.tgz(r-4.3-emscripten)
genomeIntervals.pdf |genomeIntervals.html✨
genomeIntervals/json (API)
NEWS
| # Install 'genomeIntervals' in R: |
| install.packages('genomeIntervals', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:genomeIntervals-1.63.0(bioc 3.21)genomeIntervals-1.62.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
dataimportinfrastructuregenetics
Last updated 2 months agofrom:ebab91308d. Checks:OK: 1 WARNING: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 30 2024 |
| R-4.5-win | WARNING | Nov 30 2024 |
| R-4.5-linux | WARNING | Nov 30 2024 |
| R-4.4-win | WARNING | Nov 30 2024 |
| R-4.4-mac | WARNING | Nov 30 2024 |
| R-4.3-win | WARNING | Nov 30 2024 |
| R-4.3-mac | WARNING | Nov 30 2024 |
Exports:annotationannotation<-coercecore_annotateddistance_to_nearestGenomeIntervalsgetGffAttributeinter_baseinter_base<-interval_complementinterval_intersectioninterval_overlapinterval_unionparseGffAttributesreadBasePairFeaturesGff3readGff3readZeroLengthFeaturesGff3seq_nameseq_name<-seqnamesseqnames<-showsizestrandstrand<-type<-which_nearestwidthwriteGff3
Dependencies:askpassBiocGenericscurlgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangeshttrintervalsIRangesjsonlitemimeopensslR6S4VectorssysUCSC.utilsXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Operations on genomic intervals | genomeIntervals-package genomeIntervals |
| c extension for the 'genomeIntervals package' | c c,Genome_intervals-method c,Genome_intervals_stranded-method |
| Genome intervals with minimal annotation | core_annotated core_annotated,Genome_intervals-method core_annotated,Genome_intervals_stranded-method |
| Distance in bases to the closest interval(s) | distance_to_nearest distance_to_nearest,Genome_intervals,Genome_intervals-method distance_to_nearest,Genome_intervals_stranded,Genome_intervals_stranded-method |
| Genome Intervals examples | gen_ints i j k |
| The following function have been deprecated: • 'seq_name' • 'seq_name<-' | Genome_intervals deprecated functions seq_name seq_name,Genome_intervals-method seq_name<- seq_name<-,Genome_intervals-method |
| Class "Genome\_intervals\_stranded" | coerce,Genome_intervals_stranded,character-method Genome_intervals_stranded-class strand strand,Genome_intervals_stranded-method strand<- strand<-,Genome_intervals_stranded-method |
| Class "Genome\_intervals" | $,Genome_intervals-method $<-,Genome_intervals-method annotation annotation,Genome_intervals-method annotation<- annotation<-,Genome_intervals-method coerce,Genome_intervals,character-method coerce,Genome_intervals,data.frame-method coerce,Genome_intervals,Intervals_full-method Genome_intervals-class inter_base inter_base,Genome_intervals-method inter_base<- inter_base<-,Genome_intervals-method seqnames,Genome_intervals-method seqnames<-,Genome_intervals-method show,Genome_intervals-method size,Genome_intervals-method strand<-,Genome_intervals_stranded,ANY-method type<-,Genome_intervals-method which_nearest,Genome_intervals,Genome_intervals-method width,Genome_intervals-method [,Genome_intervals,ANY-method [,Genome_intervals-method [<-,Genome_intervals,ANY,missing,Genome_intervals-method [[,Genome_intervals,ANY,ANY-method [[,Genome_intervals,ANY-method [[,Genome_intervals-method [[<-,Genome_intervals,ANY,ANY-method [[<-,Genome_intervals,ANY-method [[<-,Genome_intervals-method |
| Ordering methods for Genome intervals | Genome_intervals-ordering order order,Genome_intervals-method order,Genome_intervals_stranded-method rank rank,Genome_intervals-method rank,Genome_intervals_stranded-method sort sort,Genome_intervals-method sort,Genome_intervals_stranded-method xtfrm xtfrm,Genome_intervals-method xtfrm,Genome_intervals_stranded-method |
| Constructor function for genomeIntervals objects | GenomeIntervals GenomeIntervals-constructor |
| Coercion methods of the genomeIntervals package | as as,Genome_intervals,GRangesList-method as,Genome_intervals-method coerce,Genome_intervals,GRanges-method coerce,Genome_intervals,GRangesList-method genomeIntervals coercion methods |
| Pull one or more key/value pairs from gffAttributes strings | getGffAttribute |
| Assess overlap from one set of genomic intervals to another | interval_overlap interval_overlap,ANY,missing-method interval_overlap,Genome_intervals,Genome_intervals-method interval_overlap,Genome_intervals_stranded,Genome_intervals_stranded-method interval_overlap,missing,ANY-method |
| Genome interval set operations | interval_complement interval_complement,Genome_intervals-method interval_complement,Genome_intervals_stranded-method interval_intersection interval_intersection,Genome_intervals-method interval_intersection,Genome_intervals_stranded-method interval_union interval_union,Genome_intervals-method interval_union,Genome_intervals_stranded-method |
| Parse out the gffAttributes column of a Genome\_intervals object | parseGffAttributes |
| readGff3 | .readGff3 readBasePairFeaturesGff3 readBasePairFeaturesGff3,character-method readGff3 readGff3,character-method readZeroLengthFeaturesGff3 readZeroLengthFeaturesGff3,character-method writeGff3 writeGff3,data.frame-method writeGff3,Genome_intervals-method |
