Package: BiocNeighbors 1.99.2

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 or with vantage point trees. Approximate searches can be performed using the Annoy or HNSW libraries. Searching on either Euclidean or Manhattan distances is supported. Parallelization is achieved for all methods by using BiocParallel. Functions are also provided to search for all neighbors within a given distance.

Authors:Aaron Lun [aut, cre, cph]

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BiocNeighbors.pdf |BiocNeighbors.html
BiocNeighbors/json (API)
NEWS

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

Peer review:

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

On BioConductor:BiocNeighbors-1.99.1(bioc 3.20)BiocNeighbors-1.22.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

clusteringclassification

21 exports 9.89 score 2 dependencies 85 dependents 572 scripts 17.6k downloads

Last updated 7 days agofrom:3faa79470b. Checks:OK: 7 WARNING: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 07 2024
R-4.5-win-x86_64WARNINGOct 07 2024
R-4.5-linux-x86_64OKOct 07 2024
R-4.4-win-x86_64WARNINGOct 07 2024
R-4.4-mac-x86_64OKOct 07 2024
R-4.4-mac-aarch64OKOct 07 2024
R-4.3-win-x86_64OKOct 07 2024
R-4.3-mac-x86_64OKOct 07 2024
R-4.3-mac-aarch64OKOct 07 2024

Exports:AnnoyIndexAnnoyParambndistancebuildIndexdefineBuilderExhaustiveIndexExhaustiveParamfindDistancefindKNNfindMutualNNfindNeighborsHnswIndexHnswParamKmknnIndexKmknnParamqueryDistancequeryKNNqueryNeighborsshowVptreeIndexVptreeParam

Dependencies:assortheadRcpp

Finding neighbors in high-dimensional space

Rendered fromuserguide.Rmdusingknitr::rmarkdownon Oct 07 2024.

Last update: 2024-10-06
Started: 2024-09-05

Readme and manuals

Help Manual

Help pageTopics
BiocNeighbors: Nearest Neighbor Detection for Bioconductor PackagesBiocNeighbors-package BiocNeighbors
The AnnoyParam classAnnoyIndex AnnoyIndex-class AnnoyParam AnnoyParam-class defineBuilder,AnnoyParam-method show,AnnoyParam-method
The BiocNeighborIndex classBiocNeighborIndex BiocNeighborIndex-class show,BiocNeighborIndex-method
The BiocNeighborParam classBiocNeighborParam BiocNeighborParam-class bndistance show,BiocNeighborParam-method [[,BiocNeighborParam-method [[<-,BiocNeighborParam-method
Build a nearest-neighbor indexbuildIndex buildIndex,matrix,BiocNeighborParam-method buildIndex,matrix,list-method buildIndex,matrix,missing-method buildIndex,matrix,NULL-method
Define an index builderdefineBuilder defineBuilder,missing-method defineBuilder,NULL-method
The ExhaustiveParam classdefineBuilder,ExhaustiveParam-method ExhaustiveIndex ExhaustiveIndex-class ExhaustiveParam ExhaustiveParam-class
Distance to the k-th nearest neighborfindDistance findDistance,BiocNeighborIndex,ANY-method findDistance,BiocNeighborIndex-method findDistance,matrix,ANY-method findDistance,matrix-method
Find k-nearest neighborsfindKNN findKNN,BiocNeighborIndex,ANY-method findKNN,BiocNeighborIndex-method findKNN,matrix,ANY-method findKNN,matrix-method findKNN,missing,ANY-method findKNN,missing-method
Find mutual nearest neighborsfindMutualNN
Find neighbors within a threshold distancefindNeighbors findNeighbors,BiocNeighborIndex,ANY-method findNeighbors,BiocNeighborIndex-method findNeighbors,matrix,ANY-method findNeighbors,matrix-method findNeighbors,missing,ANY-method findNeighbors,missing-method
The HnswParam classdefineBuilder,HnswParam-method HnswIndex HnswIndex-class HnswParam HnswParam-class show,HnswParam-method
The KmknnParam classdefineBuilder,KmknnParam-method KmknnIndex KmknnIndex-class KmknnParam KmknnParam-class
Distance to the k-th nearest neighbor to query pointsqueryDistance queryDistance,BiocNeighborIndex,ANY-method queryDistance,BiocNeighborIndex-method queryDistance,matrix,ANY-method queryDistance,matrix-method
Query k-nearest neighborsqueryKNN queryKNN,BiocNeighborIndex,ANY-method queryKNN,BiocNeighborIndex-method queryKNN,matrix,ANY-method queryKNN,matrix-method queryKNN,missing,ANY-method queryKNN,missing-method
Query neighbors within a threshold distancequeryNeighbors queryNeighbors,BiocNeighborIndex,ANY-method queryNeighbors,BiocNeighborIndex-method queryNeighbors,matrix,ANY-method queryNeighbors,matrix-method queryNeighbors,missing,ANY-method queryNeighbors,missing-method
The VptreeParam classdefineBuilder,VptreeParam-method VptreeIndex VptreeIndex-class VptreeParam VptreeParam-class