Package: superintervalsr 0.99.7

Kez Cleal

superintervalsr: Fast, Memory-Efficient Interval Operations for Genomics

Provides a fast, memory-efficient data structure for interval intersection queries using a novel superset-index approach. SuperIntervals maintains intervals in position-sorted order, enabling cache-friendly searches and SIMD-optimized counting operations. Chromosome- and strand-aware indexes support repeated genomic queries while retaining GRanges metadata.

Authors:Kez Cleal [aut, cre]

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superintervalsr_0.99.7.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
superintervalsr/json (API)

# Install 'superintervalsr' in R:
install.packages('superintervalsr', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/kcleal/superintervalsr/issues

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

Conda:

infrastructuredatarepresentationgenomeannotationsequencingcpp

3.30 score 7 scripts 35 exports 7 dependencies

Last updated from:cdc952b28e. Checks:1 NOTE, 15 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE201
linux-devel-arm64OK144
linux-devel-x86_64OK169
source / vignettesOK235
linux-release-arm64OK152
linux-release-x86_64OK182
macos-release-arm64OK161
macos-release-x86_64OK343
macos-oldrel-arm64OK138
macos-oldrel-x86_64OK340
windows-devel-arm64OK238
windows-devel-x86_64OK204
windows-release-arm64OK262
windows-release-x86_64OK165
windows-oldrel-x86_64OK172
wasm-releaseOK107

Exports:addas_grangesatbuildclearcountcount.batchcountOverlapscoveragedata_atdifferenceends_atexpandfindOverlapsflankgapshas_overlapsintersectionIntervalMapmerge_overlapsreservesearch_idxssearch_idxs.batchsearch_itemssearch_keyssearch_pointsearch_valuesshowsizespanstarts_atSuperIntervalMapsymmetric_differenceunion_withunique_intervals

Dependencies:BiocGenericsgenericsGenomicRangesIRangesRcppS4VectorsSeqinfo

SuperIntervals with Bioconductor: genomic overlap workflows
Annotating peaks with genes | Retrieving source rows after indexing | Set operations for covered regions and nearby features | Repeated queries | A real RNA-seq example: promoter overlaps in airway cells
Rendered fromworkflows.Rmdusingknitr::rmarkdown

Last update: 2026-10-14
Started: 2025-07-23

Getting Started with SuperIntervals
Introduction | Basic Usage | Creating and Building an IntervalMap | Searching for Overlaps | Query Statistics | Accessing Individual Intervals | Set operations | Performance Tips | Use Cases | Session Information
Rendered fromgetting-started.Rmdusingknitr::rmarkdown

Last update: 2026-10-14
Started: 2025-07-03

Readme and manuals

Help Manual

Help pageTopics
Access interval at specific index[.IntervalMap
Add an interval to the mapadd
Convert IntervalMap items result back to GRangesas_granges
Get interval at specific indexat
Build index for efficient queriesbuild
Clear all intervalsclear
Count overlapping intervalscount
Count overlaps for multiple rangescount.batch
Get coverage statistics for a rangecoverage
Get data at specific indexdata_at
Difference of two interval setsdifference
Get end position at specific indexends_at
Expand each interval by fixed amountsexpand
Query an indexed genomic subjectcountOverlaps,GRanges,SuperIntervalMap-method findOverlaps,GRanges,SuperIntervalMap-method
Create flanking intervals beside each intervalflank
Find gaps within a rangegaps
Check if any intervals overlap with a rangehas_overlaps
Intersection of two interval setsintersection
Create a new IntervalMapIntervalMap IntervalMap.data.frame IntervalMap.default IntervalMap.GRanges IntervalMap.integer IntervalMap.numeric
Get the length of an IntervalMaplength.IntervalMap
Merge overlapping intervalsmerge_overlaps
Print method for IntervalMapprint.IntervalMap
Reserve space for intervalsreserve
Search for indices of overlapping intervalssearch_idxs
Batch search for indicessearch_idxs.batch
Search for complete items (start, end, value) of overlapping intervalssearch_items
Search for keys (start, end pairs) of overlapping intervalssearch_keys
Search for values at a single pointsearch_point
Search for values in overlapping intervalssearch_values
Get number of intervalssize
Span of all intervalsspan
Get start position at specific indexstarts_at
Create an indexed genomic subjectSuperIntervalMap
An indexed collection of genomic rangeslength,SuperIntervalMap-method show,SuperIntervalMap-method SuperIntervalMap-class
Symmetric difference of two interval setssymmetric_difference
Union of two interval setsunion_with
Remove duplicate intervalsunique_intervals