recipe bioconductor-cytomds

Low Dimensions projection of cytometry samples

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-cytomds/meta.yaml

This package implements a low dimensional visualization of a set of cytometry samples, in order to visually assess the 'distances' between them. This, in turn, can greatly help the user to identify quality issues like batch effects or outlier samples, and/or check the presence of potential sample clusters that might align with the exeprimental design. The CytoMDS algorithm combines, on the one hand, the concept of Earth Mover's Distance (EMD), a.k.a. Wasserstein metric and, on the other hand, the Multi Dimensional Scaling (MDS) algorithm for the low dimensional projection. Also, the package provides some diagnostic tools for both checking the quality of the MDS projection, as well as tools to help with the interpretation of the axes of the projection.

package bioconductor-cytomds

versions:

1.2.0-0

depends bioconductor-biocparallel:

>=1.40.0,<1.41.0

depends bioconductor-cytopipeline:

>=1.6.0,<1.7.0

depends bioconductor-flowcore:

>=2.18.0,<2.19.0

depends r-base:

>=4.4,<4.5.0a0

depends r-ggforce:

depends r-ggplot2:

depends r-ggrepel:

depends r-patchwork:

depends r-pracma:

depends r-reshape2:

depends r-rlang:

depends r-smacof:

depends r-transport:

depends r-withr:

requirements:

additional platforms:

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-cytomds

and update with::

   mamba update bioconductor-cytomds

To create a new environment, run:

mamba create --name myenvname bioconductor-cytomds

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-cytomds:<tag>

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

Download stats

Link to this page

Render an badge with the following MarkDown:

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