recipe bioconductor-treekor

Cytometry Cluster Hierarchy and Cellular-to-phenotype Associations

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-treekor/meta.yaml

treekoR is a novel framework that aims to utilise the hierarchical nature of single cell cytometry data to find robust and interpretable associations between cell subsets and patient clinical end points. These associations are aimed to recapitulate the nested proportions prevalent in workflows inovlving manual gating, which are often overlooked in workflows using automatic clustering to identify cell populations. We developed treekoR to: Derive a hierarchical tree structure of cell clusters; quantify a cell types as a proportion relative to all cells in a sample (%total), and, as the proportion relative to a parent population (%parent); perform significance testing using the calculated proportions; and provide an interactive html visualisation to help highlight key results.

package bioconductor-treekor

versions:

1.10.0-0,  1.8.0-0,  1.6.0-0,  1.2.0-0,  1.0.0-0

depends bioconductor-diffcyt:

>=1.22.0,<1.23.0

depends bioconductor-edger:

>=4.0.0,<4.1.0

depends bioconductor-ggtree:

>=3.10.0,<3.11.0

depends bioconductor-hopach:

>=2.62.0,<2.63.0

depends bioconductor-singlecellexperiment:

>=1.24.0,<1.25.0

depends r-ape:

depends r-base:

>=4.3,<4.4.0a0

depends r-data.table:

depends r-dplyr:

depends r-ggiraph:

depends r-ggplot2:

depends r-lme4:

depends r-multcomp:

depends r-patchwork:

depends r-tidyr:

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-treekor

and update with::

   mamba update bioconductor-treekor

To create a new environment, run:

mamba create --name myenvname bioconductor-treekor

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-treekor:<tag>

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

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-treekor/README.html)