recipe bioconductor-cytoglmm

Conditional Differential Analysis for Flow and Mass Cytometry Experiments

Homepage:

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

License:

LGPL-3

Recipe:

/bioconductor-cytoglmm/meta.yaml

The CytoGLMM R package implements two multiple regression strategies: A bootstrapped generalized linear model (GLM) and a generalized linear mixed model (GLMM). Most current data analysis tools compare expressions across many computationally discovered cell types. CytoGLMM focuses on just one cell type. Our narrower field of application allows us to define a more specific statistical model with easier to control statistical guarantees. As a result, CytoGLMM finds differential proteins in flow and mass cytometry data while reducing biases arising from marker correlations and safeguarding against false discoveries induced by patient heterogeneity.

package bioconductor-cytoglmm

versions:

1.14.0-0,  1.10.0-0,  1.8.0-0,  1.6.0-0,  1.2.0-0,  1.0.0-0

depends bioconductor-biocparallel:

>=1.40.0,<1.41.0

depends r-base:

>=4.4,<4.5.0a0

depends r-caret:

depends r-cowplot:

depends r-doparallel:

depends r-dplyr:

depends r-factoextra:

depends r-flexmix:

depends r-ggplot2:

depends r-ggrepel:

depends r-logging:

depends r-magrittr:

depends r-mass:

depends r-matrix:

depends r-mbest:

depends r-pheatmap:

depends r-rcolorbrewer:

depends r-rlang:

depends r-stringr:

depends r-strucchange:

depends r-tibble:

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-cytoglmm

and update with::

   mamba update bioconductor-cytoglmm

To create a new environment, run:

mamba create --name myenvname bioconductor-cytoglmm

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-cytoglmm:<tag>

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

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