recipe bioconductor-compass

Combinatorial Polyfunctionality Analysis of Single Cells

Homepage:

https://bioconductor.org/packages/3.18/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:

1.40.0-0,  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, 

1.40.0-0,  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 bioconductor-biocstyle:

>=2.30.0,<2.31.0

depends bioconductor-biocstyle:

>=2.30.0,<2.31.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx-ng:

>=12

depends r-abind:

depends r-base:

>=4.3,<4.4.0a0

depends r-clue:

depends r-coda:

depends r-data.table:

depends r-dplyr:

depends r-foreach:

depends r-knitr:

depends r-magrittr:

depends r-pdist:

depends r-plyr:

depends r-rcolorbrewer:

depends r-rcpp:

>=0.11.0

depends r-reshape2:

depends r-rlang:

depends r-rmarkdown:

depends r-scales:

depends r-tidyr:

requirements:

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-compass

and update with::

   mamba update bioconductor-compass

To create a new environment, run:

mamba create --name myenvname bioconductor-compass

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-compass:<tag>

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

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