Package: BiocNeighbors 2.1.0
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_2.1.0.tar.gz
BiocNeighbors_2.1.0.zip(r-4.5)BiocNeighbors_2.1.0.zip(r-4.4)BiocNeighbors_2.1.0.zip(r-4.3)
BiocNeighbors_2.1.0.tgz(r-4.4-x86_64)BiocNeighbors_2.1.0.tgz(r-4.4-arm64)BiocNeighbors_2.1.0.tgz(r-4.3-x86_64)BiocNeighbors_2.1.0.tgz(r-4.3-arm64)
BiocNeighbors_2.1.0.tar.gz(r-4.5-noble)BiocNeighbors_2.1.0.tar.gz(r-4.4-noble)
BiocNeighbors_2.1.0.tgz(r-4.4-emscripten)BiocNeighbors_2.1.0.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-1.99.3(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 23 days agofrom:06559d5bf0. Checks:OK: 7 WARNING: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 30 2024 |
| R-4.5-win-x86_64 | WARNING | Oct 30 2024 |
| R-4.5-linux-x86_64 | OK | Oct 30 2024 |
| R-4.4-win-x86_64 | WARNING | Oct 30 2024 |
| R-4.4-mac-x86_64 | OK | Oct 30 2024 |
| R-4.4-mac-aarch64 | OK | Oct 30 2024 |
| R-4.3-win-x86_64 | OK | Oct 30 2024 |
| R-4.3-mac-x86_64 | OK | Oct 30 2024 |
| R-4.3-mac-aarch64 | OK | Oct 30 2024 |
Exports:AnnoyIndexAnnoyParambndistancebuildIndexdefineBuilderExhaustiveIndexExhaustiveParamfindDistancefindKNNfindMutualNNfindNeighborsHnswIndexHnswParamKmknnIndexKmknnParamqueryDistancequeryKNNqueryNeighborsshowVptreeIndexVptreeParam
Dependencies:assortheadRcpp
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,matrix,BiocNeighborParam-method buildIndex,matrix,list-method buildIndex,matrix,missing-method buildIndex,matrix,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 findDistance,BiocNeighborGenericIndex,ANY-method findDistance,BiocNeighborGenericIndex-method findDistance,matrix,ANY-method findDistance,matrix-method |
| Find k-nearest neighbors | findKNN findKNN,BiocNeighborGenericIndex,ANY-method findKNN,BiocNeighborGenericIndex-method findKNN,matrix,ANY-method findKNN,matrix-method findKNN,missing,ANY-method findKNN,missing-method |
| Find mutual nearest neighbors | findMutualNN |
| Find neighbors within a threshold distance | findNeighbors findNeighbors,BiocNeighborGenericIndex,ANY-method findNeighbors,BiocNeighborGenericIndex-method findNeighbors,matrix,ANY-method findNeighbors,matrix-method findNeighbors,missing,ANY-method findNeighbors,missing-method |
| 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 |
| Distance to the k-th nearest neighbor to query points | queryDistance queryDistance,BiocNeighborGenericIndex,ANY-method queryDistance,BiocNeighborGenericIndex-method queryDistance,matrix,ANY-method queryDistance,matrix-method |
| Query k-nearest neighbors | queryKNN queryKNN,BiocNeighborGenericIndex,ANY-method queryKNN,BiocNeighborGenericIndex-method queryKNN,matrix,ANY-method queryKNN,matrix-method queryKNN,missing,ANY-method queryKNN,missing-method |
| Query neighbors within a threshold distance | queryNeighbors queryNeighbors,BiocNeighborGenericIndex,ANY-method queryNeighbors,BiocNeighborGenericIndex-method queryNeighbors,matrix,ANY-method queryNeighbors,matrix-method queryNeighbors,missing,ANY-method queryNeighbors,missing-method |
| The VptreeParam class | defineBuilder,VptreeParam-method VptreeIndex VptreeIndex-class VptreeParam VptreeParam-class |
