recipe bioconductor-samspectral

Identifies cell population in flow cytometry data

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/SamSPECTRAL.html

License:

GPL (>= 2)

Recipe:

/bioconductor-samspectral/meta.yaml

Samples large data such that spectral clustering is possible while preserving density information in edge weights. More specifically, given a matrix of coordinates as input, SamSPECTRAL first builds the communities to sample the data points. Then, it builds a graph and after weighting the edges by conductance computation, the graph is passed to a classic spectral clustering algorithm to find the spectral clusters. The last stage of SamSPECTRAL is to combine the spectral clusters. The resulting "connected components" estimate biological cell populations in the data. See the vignette for more details on how to use this package, some illustrations, and simple examples.

package bioconductor-samspectral

(downloads) docker_bioconductor-samspectral

versions:
1.56.0-1,  1.56.0-0,  1.54.0-0,  1.52.0-1,  1.52.0-0,  1.48.0-2,  1.48.0-1,  1.48.0-0,  1.46.0-0, 

1.56.0-1,  1.56.0-0,  1.54.0-0,  1.52.0-1,  1.52.0-0,  1.48.0-2,  1.48.0-1,  1.48.0-0,  1.46.0-0,  1.44.0-1,  1.44.0-0,  1.42.0-0,  1.40.0-0,  1.38.0-1,  1.38.0-0,  1.36.1-0,  1.36.0-0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends r-base:

>=4.3,<4.4.0a0

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-samspectral

and update with::

   mamba update bioconductor-samspectral

To create a new environment, run:

mamba create --name myenvname bioconductor-samspectral

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

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

(see `bioconductor-samspectral/tags`_ for valid values for ``<tag>``)

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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-samspectral/README.html)