recipe bioconductor-flowspecs

Tools for processing of high-dimensional cytometry data

Homepage:

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

License:

MIT + file LICENSE

Recipe:

/bioconductor-flowspecs/meta.yaml

This package is intended to fill the role of conventional cytometry pre-processing software, for spectral decomposition, transformation, visualization and cleanup, and to aid further downstream analyses, such as with DepecheR, by enabling transformation of flowFrames and flowSets to dataframes. Functions for flowCore-compliant automatic 1D-gating/filtering are in the pipe line. The package name has been chosen both as it will deal with spectral cytometry and as it will hopefully give the user a nice pair of spectacles through which to view their data.

package bioconductor-flowspecs

(downloads) docker_bioconductor-flowspecs

Versions:
1.24.0-0,  1.20.0-0,  1.16.0-0,  1.14.0-0,  1.12.0-0,  1.8.0-0,  1.6.0-0,  1.4.0-1,  1.4.0-0, 

1.24.0-0,  1.20.0-0,  1.16.0-0,  1.14.0-0,  1.12.0-0,  1.8.0-0,  1.6.0-0,  1.4.0-1,  1.4.0-0,  1.2.0-0,  1.0.0-0

Depends:

  • on bioconductor-biobase >=2.70.0,<2.71.0

  • on bioconductor-biocgenerics >=0.56.0,<0.57.0

  • on bioconductor-biocparallel >=1.44.0,<1.45.0

  • on bioconductor-flowcore >=2.22.0,<2.23.0

  • on r-base >=4.5,<4.6.0a0

  • on r-ggplot2 >=3.1.0

  • on r-reshape2 >=1.4.3

  • on r-zoo >=1.8.6

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-flowspecs

to add into an existing workspace instead, run:

pixi add bioconductor-flowspecs

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-flowspecs

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-flowspecs

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-flowspecs:<tag>

(see bioconductor-flowspecs/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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Render an install-with-bioconda badge with the following MarkDown:

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