- recipe bioconductor-cytoglmm
Conditional Differential Analysis for Flow and Mass Cytometry Experiments
- Homepage:
https://bioconductor.org/packages/3.20/bioc/html/CytoGLMM.html
- License:
LGPL-3
- Recipe:
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:
1.18.0-0,1.14.0-0,1.10.0-0,1.8.0-0,1.6.0-0,1.2.0-0,1.0.0-0- Depends:
on bioconductor-biocparallel
>=1.44.0,<1.45.0on r-base
>=4.5,<4.6.0a0on r-caret
on r-cowplot
on r-doparallel
on r-dplyr
on r-factoextra
on r-flexmix
on r-ggplot2
on r-ggrepel
on r-logging
on r-magrittr
on r-mass
on r-matrix
on r-mbest
on r-pheatmap
on r-rcolorbrewer
on r-rlang
on r-stringr
on r-strucchange
on r-tibble
on r-tidyr
- 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-cytoglmm
to add into an existing workspace instead, run:
pixi add bioconductor-cytoglmm
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-cytoglmm
Alternatively, to install into a new environment, run:
conda create -n envname bioconductor-cytoglmm
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-cytoglmm:<tag>
(see bioconductor-cytoglmm/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:
[](http://bioconda.github.io/recipes/bioconductor-cytoglmm/README.html)
