Overview | Finding nearest neighbors | Finding all neighbors within range | Saving indices to disk | Usage in downstream C++ libraries | Extending to new methods | Introduction | In R | In C++ | Session information
Package: BiocNeighbors 2.7.2
Aaron Lun
BiocNeighbors: Nearest Neighbor Detection for Bioconductor Packages
Implements exact and approximate methods for nearest neighbor detection, in a framework that allows them to be easily switched within Bioconductor packages or workflows. Exact searches can be performed using the k-means for k-nearest neighbors algorithm, vantage point trees, or an exhaustive search. Approximate searches can be performed using the Annoy or HNSW libraries. Each search can be performed with a variety of different distance metrics, parallelization, and variable numbers of neighbors. Range-based searches (to find all neighbors within a certain distance) are also supported.
Authors:
BiocNeighbors_2.7.2.tar.gz
BiocNeighbors_2.7.2.zip(r-4.7)BiocNeighbors_2.7.2.zip(r-4.6)BiocNeighbors_2.7.2.zip(r-4.5)
BiocNeighbors_2.7.2.tgz(r-4.6-x86_64)BiocNeighbors_2.7.2.tgz(r-4.6-arm64)BiocNeighbors_2.7.2.tgz(r-4.5-x86_64)BiocNeighbors_2.7.2.tgz(r-4.5-arm64)
BiocNeighbors_2.7.2.tar.gz(r-4.7-arm64)BiocNeighbors_2.7.2.tar.gz(r-4.7-x86_64)BiocNeighbors_2.7.2.tar.gz(r-4.6-arm64)BiocNeighbors_2.7.2.tar.gz(r-4.6-x86_64)
BiocNeighbors_2.7.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
BiocNeighbors/json (API)
| # Install 'BiocNeighbors' in R: |
| install.packages('BiocNeighbors', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/knncolle/biocneighbors/issues
On BioConductor:BiocNeighbors-2.7.2(bioc 3.24)BiocNeighbors-2.6.0(bioc 3.23)
clusteringclassificationbioconductor-packagehuman-cell-atlasnearest-neighbor-searchcpp
Last updated from:b17cc73d44. Checks:1 WARNING, 13 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 333 | ||
| linux-devel-arm64 | OK | 284 | ||
| linux-devel-x86_64 | OK | 295 | ||
| source / vignettes | OK | 415 | ||
| linux-release-arm64 | OK | 256 | ||
| linux-release-x86_64 | OK | 288 | ||
| macos-release-arm64 | OK | 119 | ||
| macos-release-x86_64 | OK | 471 | ||
| macos-oldrel-arm64 | OK | 158 | ||
| macos-oldrel-x86_64 | OK | 289 | ||
| windows-devel | OK | 180 | ||
| windows-release | OK | 186 | ||
| windows-oldrel | OK | 210 | ||
| wasm-release | OK | 267 |
Exports:AnnoyIndexAnnoyParambndistancebuildIndexdefineBuilderExhaustiveIndexExhaustiveParamfindDistancefindDistanceFromIndexfindKNNfindKnnFromIndexfindMutualNNfindNeighborsfindNeighborsFromIndexfindResultsToHitsfindResultsToMatrixgetLoadGenericIndexRegistryHnswIndexHnswParamKmknnIndexKmknnParamloadIndexqueryDistancequeryDistanceFromIndexqueryKNNqueryKnnFromIndexqueryNeighborsqueryNeighborsFromIndexqueryResultsToHitsqueryResultsToMatrixregisterLoadGenericIndexClassregisterLoadIndexFunctionsaveIndexshowVptreeIndexVptreeParam
Dependencies:abindassortheadbeachmatBiocGenericsDelayedArraygenericsIRangeslatticeMatrixMatrixGenericsmatrixStatsRcppS4ArraysS4VectorsSparseArrayXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| BiocNeighbors: Nearest Neighbor Detection for Bioconductor Packages | BiocNeighbors-package BiocNeighbors |
| The AnnoyParam class | AnnoyIndex AnnoyIndex-class AnnoyParam AnnoyParam-class defineBuilder,AnnoyParam-method show,AnnoyParam-method |
| The BiocNeighborIndex class | BiocNeighborGenericIndex-class BiocNeighborIndex BiocNeighborIndex-class show,BiocNeighborIndex-method |
| The BiocNeighborParam class | BiocNeighborParam BiocNeighborParam-class bndistance show,BiocNeighborParam-method [[,BiocNeighborParam-method [[<-,BiocNeighborParam-method |
| Build a nearest-neighbor index | buildIndex buildIndex,BiocNeighborParam-method buildIndex,list-method buildIndex,missing-method buildIndex,NULL-method |
| Define an index builder | defineBuilder defineBuilder,missing-method defineBuilder,NULL-method |
| The ExhaustiveParam class | defineBuilder,ExhaustiveParam-method ExhaustiveIndex ExhaustiveIndex-class ExhaustiveParam ExhaustiveParam-class |
| Distance to the k-th nearest neighbor | findDistance findDistanceFromIndex findDistanceFromIndex,BiocNeighborGenericIndex-method |
| Find k-nearest neighbors | findKNN findKnnFromIndex findKnnFromIndex,BiocNeighborGenericIndex-method |
| Find mutual nearest neighbors | findMutualNN |
| Find neighbors within a threshold distance | findNeighbors findNeighborsFromIndex findNeighborsFromIndex,BiocNeighborGenericIndex-method |
| Convert neighbor search results to alternative representations | findResultsToHits findResultsToMatrix queryResultsToHits queryResultsToMatrix |
| Load indices from extension packages | getLoadGenericIndexRegistry registerLoadGenericIndexClass registerLoadIndexFunction |
| The HnswParam class | defineBuilder,HnswParam-method HnswIndex HnswIndex-class HnswParam HnswParam-class show,HnswParam-method |
| The KmknnParam class | defineBuilder,KmknnParam-method KmknnIndex KmknnIndex-class KmknnParam KmknnParam-class |
| Load a prebuilt search index from disk | loadIndex |
| Distance to the k-th nearest neighbor to query points | queryDistance queryDistanceFromIndex queryDistanceFromIndex,BiocNeighborGenericIndex-method |
| Query k-nearest neighbors | queryKNN queryKnnFromIndex queryKnnFromIndex,BiocNeighborGenericIndex-method |
| Query neighbors within a threshold distance | queryNeighbors queryNeighborsFromIndex queryNeighborsFromIndex,BiocNeighborGenericIndex-method |
| Save a nearest-neighbor index | saveIndex saveIndex,BiocNeighborGenericIndex-method |
| The VptreeParam class | defineBuilder,VptreeParam-method VptreeIndex VptreeIndex-class VptreeParam VptreeParam-class |
