recipe bioconductor-biocneighbors

Nearest Neighbor Detection for Bioconductor Packages

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/BiocNeighbors.html

License:

GPL-3

Recipe:

/bioconductor-biocneighbors/meta.yaml

Links:

biotools: biocneighbors, usegalaxy-eu: biocneighbors

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.

package bioconductor-biocneighbors

(downloads) docker_bioconductor-biocneighbors

Versions:
2.4.0-0,  2.0.0-1,  2.0.0-0,  1.20.0-1,  1.20.0-0,  1.18.0-0,  1.16.0-1,  1.16.0-0,  1.12.0-2, 

2.4.0-0,  2.0.0-1,  2.0.0-0,  1.20.0-1,  1.20.0-0,  1.18.0-0,  1.16.0-1,  1.16.0-0,  1.12.0-2,  1.12.0-1,  1.12.0-0,  1.10.0-0,  1.8.2-0,  1.8.0-0,  1.6.0-0,  1.4.0-0,  1.2.0-1,  1.0.0-0

Depends:

  • on bioconductor-assorthead >=1.4.0,<1.5.0

  • on bioconductor-assorthead >=1.4.0,<1.5.0a0

  • on libblas >=3.9.0,<4.0a0

  • on libgcc >=14

  • on liblapack >=3.9.0,<4.0a0

  • on liblzma >=5.8.2,<6.0a0

  • on libstdcxx >=14

  • on libzlib >=1.3.1,<2.0a0

  • on r-base >=4.5,<4.6.0a0

  • on r-rcpp

Additional platforms:
linux-aarch64,  osx-arm64

Installation

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-biocneighbors

to add into an existing workspace instead, run:

pixi add bioconductor-biocneighbors

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-biocneighbors

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-biocneighbors

with envname being the name of the desired environment.

Container

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/bioconductor-biocneighbors:<tag>

(see bioconductor-biocneighbors/tags for valid values for <tag>).

Integrated deployment

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats

Link to this page

Render an install-with-bioconda badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-biocneighbors/README.html)