recipe bioconductor-samspectral

Identifies cell population in flow cytometry data

Homepage:

https://bioconductor.org/packages/3.20/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:
1.64.0-0,  1.60.0-0,  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, 

1.64.0-0,  1.60.0-0,  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:

  • 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 libzlib >=1.3.1,<2.0a0

  • on r-base >=4.5,<4.6.0a0

Additional platforms:

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-samspectral

to add into an existing workspace instead, run:

pixi add bioconductor-samspectral

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-samspectral

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-samspectral

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-samspectral:<tag>

(see bioconductor-samspectral/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.

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