Package Recipe 'bioconductor-compass'

recipe bioconductor-compass

Combinatorial Polyfunctionality Analysis of Single Cells

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/COMPASS.html
License:: Artistic-2.0
Recipe:: /bioconductor-compass/meta.yaml
Links:: biotools: compass, doi: 10.1038/nbt.3187

COMPASS is a statistical framework that enables unbiased analysis of antigen-specific T-cell subsets. COMPASS uses a Bayesian hierarchical framework to model all observed cell-subsets and select the most likely to be antigen-specific while regularizing the small cell counts that often arise in multi-parameter space. The model provides a posterior probability of specificity for each cell subset and each sample, which can be used to profile a subject's immune response to external stimuli such as infection or vaccination.

package bioconductor-compass¶

Versions:

1.48.0-0, 1.44.0-0, 1.40.0-1, 1.40.0-0, 1.38.1-0, 1.36.0-1, 1.36.0-0, 1.32.0-2, 1.32.0-1,

1.48.0-0, 1.44.0-0, 1.40.0-1, 1.40.0-0, 1.38.1-0, 1.36.0-1, 1.36.0-0, 1.32.0-2, 1.32.0-1, 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, 1.20.0-0, 1.18.1-0, 1.18.0-0, 1.16.0-0

Depends:

on bioconductor-biocstyle >=2.38.0,<2.39.0
on bioconductor-biocstyle >=2.38.0,<2.39.0a0
on libblas >=3.9.0,<4.0a0
on libgcc >=14
on liblapack >=3.9.0,<4.0a0
on liblzma >=5.8.2,<6.0a0
on libstdcxx >=14
on libzlib >=1.3.1,<2.0a0
on r-abind
on r-base >=4.5,<4.6.0a0
on r-clue
on r-coda
on r-data.table
on r-dplyr
on r-foreach
on r-knitr
on r-magrittr
on r-pdist
on r-plyr
on r-rcolorbrewer
on r-rcpp >=0.11.0
on r-reshape2
on r-rlang
on r-rmarkdown
on r-scales
on r-tidyr

Additional platforms:

linux-aarch64

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-compass

to add into an existing workspace instead, run:

pixi add bioconductor-compass

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-compass

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-compass

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-compass:<tag>

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