Package: BiocNeighbors 1.23.0
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:
BiocNeighbors_1.23.0.tar.gz
BiocNeighbors_1.23.0.zip(r-4.5)BiocNeighbors_1.23.0.zip(r-4.4)BiocNeighbors_1.23.0.zip(r-4.3)
BiocNeighbors_1.23.0.tgz(r-4.4-arm64)BiocNeighbors_1.23.0.tgz(r-4.4-x86_64)BiocNeighbors_1.23.0.tgz(r-4.3-arm64)BiocNeighbors_1.23.0.tgz(r-4.3-x86_64)
BiocNeighbors_1.23.0.tar.gz(r-4.5-noble)BiocNeighbors_1.23.0.tar.gz(r-4.4-noble)
BiocNeighbors_1.23.0.tgz(r-4.4-emscripten)BiocNeighbors_1.23.0.tgz(r-4.3-emscripten)
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')) |
On BioConductor:BiocNeighbors-1.23.0(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.
Last updated 2 months agofrom:e0cd963b0f
Exports:AnnoyIndexAnnoyIndex_pathAnnoyIndex_search_multAnnoyParamAnnoyParam_directoryAnnoyParam_ntreesAnnoyParam_search_multbndatabndistancebnorderbuildAnnoybuildExhaustivebuildHnswbuildIndexbuildKmknnbuildVptreeExhaustiveIndexExhaustiveParamfindAnnoyfindExhaustivefindHnswfindKmknnfindKNNfindMutualNNfindNeighborsfindVptreeHnswIndexHnswIndex_ef_searchHnswIndex_pathHnswParamHnswParam_directoryHnswParam_ef_constructionHnswParam_ef_searchHnswParam_nlinksKmknnIndexKmknnIndex_cluster_centersKmknnIndex_cluster_infoKmknnParamKmknnParam_kmeans_argsqueryAnnoyqueryExhaustivequeryHnswqueryKmknnqueryKNNqueryNeighborsqueryVptreerangeFindExhaustiverangeFindKmknnrangeFindVptreerangeQueryExhaustiverangeQueryKmknnrangeQueryVptreeshowVptreeIndexVptreeIndex_nodesVptreeParam
Dependencies:BHBiocGenericsBiocParallelcodetoolscpp11formatRfutile.loggerfutile.optionslambda.rlatticeMatrixRcppRcppHNSWS4Vectorssnow
Detecting exact nearest neighbors
Rendered fromexact.Rmdusingknitr::rmarkdownon Jun 30 2024.Last update: 2020-04-26
Started: 2018-12-03
Detecting approximate nearest neighbors
Rendered fromapprox.Rmdusingknitr::rmarkdownon Jun 30 2024.Last update: 2019-06-06
Started: 2018-12-03
Detecting all neighbors within range
Rendered fromrange.Rmdusingknitr::rmarkdownon Jun 30 2024.Last update: 2019-06-06
Started: 2018-09-29
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| BiocNeighbors: Nearest Neighbor Detection for Bioconductor Packages | BiocNeighbors-package BiocNeighbors |
| The AnnoyIndex class | AnnoyIndex AnnoyIndex-class AnnoyIndex_path AnnoyIndex_search_mult bnorder,AnnoyIndex-method show,AnnoyIndex-method |
| The AnnoyParam class | AnnoyParam AnnoyParam-class AnnoyParam_directory AnnoyParam_ntrees AnnoyParam_search_mult show,AnnoyParam-method [[,AnnoyParam-method [[<-,AnnoyParam-method |
| The BiocNeighborIndex class | BiocNeighborIndex BiocNeighborIndex-class bndata bndata,BiocNeighborIndex-method bndistance bndistance,BiocNeighborIndex-method bnorder dim,BiocNeighborIndex-method dimnames,BiocNeighborIndex-method show,BiocNeighborIndex-method [[,BiocNeighborIndex-method |
| The BiocNeighborParam class | BiocNeighborParam BiocNeighborParam-class bndistance,BiocNeighborParam-method show,BiocNeighborParam-method [[,BiocNeighborParam-method [[<-,BiocNeighborParam-method |
| Neighbor search algorithms | BiocNeighbors-algorithms |
| Reporting raw indices | BiocNeighbors-raw-index |
| Handling tied distances | BiocNeighbors-ties |
| Build an Annoy index | buildAnnoy |
| Prepare data for an exhaustive search | buildExhaustive |
| Build a HNSW index | buildHnsw |
| Build a nearest-neighbor index | buildIndex buildIndex,AnnoyParam-method buildIndex,HnswParam-method buildIndex,KmknnParam-method buildIndex,missing-method buildIndex,VptreeParam-method |
| Pre-cluster points with k-means | buildKmknn |
| Build a VP tree | buildVptree |
| The ExhaustiveIndex class | bnorder,ExhaustiveIndex-method ExhaustiveIndex ExhaustiveIndex-class |
| The ExhaustiveParam class | ExhaustiveParam ExhaustiveParam-class |
| Find k-nearest neighbors | findKNN findKNN,AnnoyIndex,AnnoyParam-method findKNN,AnnoyIndex,missing-method findKNN,ExhaustiveIndex,ExhaustiveParam-method findKNN,ExhaustiveIndex,missing-method findKNN,HnswIndex,HnswParam-method findKNN,HnswIndex,missing-method findKNN,KmknnIndex,KmknnParam-method findKNN,KmknnIndex,missing-method findKNN,missing,AnnoyParam-method findKNN,missing,ExhaustiveParam-method findKNN,missing,HnswParam-method findKNN,missing,KmknnParam-method findKNN,missing,missing-method findKNN,missing,VptreeParam-method findKNN,VptreeIndex,missing-method findKNN,VptreeIndex,VptreeParam-method findKNN-methods |
| Find nearest neighbors | findAnnoy findExhaustive findHnsw findKmknn findKNN-functions findVptree |
| Find mutual nearest neighbors | findMutualNN |
| Find all neighbors in range | findNeighbors findNeighbors,KmknnIndex,KmknnParam-method findNeighbors,KmknnIndex,missing-method findNeighbors,missing,KmknnParam-method findNeighbors,missing,missing-method findNeighbors,missing,VptreeParam-method findNeighbors,VptreeIndex,missing-method findNeighbors,VptreeIndex,VptreeParam-method findNeighbors-methods |
| Find all neighbors in range | findNeighbors-functions rangeFindExhaustive rangeFindKmknn rangeFindVptree |
| The HnswIndex class | bnorder,HnswIndex-method HnswIndex HnswIndex-class HnswIndex_ef_search HnswIndex_path show,HnswIndex-method |
| The HnswParam class | HnswParam HnswParam-class HnswParam_directory HnswParam_ef_construction HnswParam_ef_search HnswParam_nlinks show,HnswParam-method [[,HnswParam-method [[<-,HnswParam-method |
| The KmknnIndex class | bnorder,KmknnIndex-method KmknnIndex KmknnIndex-class KmknnIndex_cluster_centers KmknnIndex_cluster_info show,KmknnIndex-method |
| The KmknnParam class | KmknnParam KmknnParam-class KmknnParam_kmeans_args show,KmknnParam-method |
| Query k-nearest neighbors | queryKNN queryKNN,AnnoyIndex,AnnoyParam-method queryKNN,AnnoyIndex,missing-method queryKNN,ExhaustiveIndex,ExhaustiveParam-method queryKNN,ExhaustiveIndex,missing-method queryKNN,HnswIndex,HnswParam-method queryKNN,HnswIndex,missing-method queryKNN,KmknnIndex,KmknnParam-method queryKNN,KmknnIndex,missing-method queryKNN,missing,AnnoyParam-method queryKNN,missing,ExhaustiveParam-method queryKNN,missing,HnswParam-method queryKNN,missing,KmknnParam-method queryKNN,missing,missing-method queryKNN,missing,VptreeParam-method queryKNN,VptreeIndex,missing-method queryKNN,VptreeIndex,VptreeParam-method queryKNN-methods |
| Query nearest neighbors | queryAnnoy queryExhaustive queryHnsw queryKmknn queryKNN-functions queryVptree |
| Query all neighbors | queryNeighbors queryNeighbors,KmknnIndex,KmknnParam-method queryNeighbors,KmknnIndex,missing-method queryNeighbors,missing,KmknnParam-method queryNeighbors,missing,missing-method queryNeighbors,missing,VptreeParam-method queryNeighbors,VptreeIndex,missing-method queryNeighbors,VptreeIndex,VptreeParam-method queryNeighbors-methods |
| Query neighbors in range | queryNeighbors-functions rangeQueryExhaustive rangeQueryKmknn rangeQueryVptree |
| The VptreeIndex class | bnorder,VptreeIndex-method VptreeIndex VptreeIndex-class VptreeIndex_nodes |
| The VptreeParam class | VptreeParam VptreeParam-class |
