Package Recipe 'bioconductor-flowmap'

recipe bioconductor-flowmap

Mapping cell populations in flow cytometry data for cross-sample comparisons using the Friedman-Rafsky Test

Homepage:: https://bioconductor.org/packages/3.17/bioc/html/flowMap.html
License:: GPL (>=2)
Recipe:: /bioconductor-flowmap/meta.yaml
Links:: biotools: flowmap, doi: 10.1002/cyto.a.22735

flowMap quantifies the similarity of cell populations across multiple flow cytometry samples using a nonparametric multivariate statistical test. The method is able to map cell populations of different size, shape, and proportion across multiple flow cytometry samples. The algorithm can be incorporate in any flow cytometry work flow that requires accurat quantification of similarity between cell populations.

package bioconductor-flowmap¶

Versions:

1.38.0-0, 1.36.0-0, 1.32.0-0, 1.30.0-0, 1.28.0-1, 1.28.0-0, 1.26.0-0, 1.24.0-0, 1.22.0-1,

1.38.0-0, 1.36.0-0, 1.32.0-0, 1.30.0-0, 1.28.0-1, 1.28.0-0, 1.26.0-0, 1.24.0-0, 1.22.0-1, 1.22.0-0, 1.20.1-0, 1.18.0-0, 1.14.0-0

Depends:

on r-abind >=1.4.0
on r-ade4 >=1.5-2
on r-base >=4.3,<4.4.0a0
on r-doparallel >=1.0.3
on r-matrix >=1.1-4
on r-reshape2 >=1.2.2
on r-scales >=0.2.3

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-flowmap

to add into an existing workspace instead, run:

pixi add bioconductor-flowmap

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-flowmap

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-flowmap

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-flowmap:<tag>

(see bioconductor-flowmap/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 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-flowmap/README.html)