recipe bioconductor-diffcyt

Differential discovery in high-dimensional cytometry via high-resolution clustering

Homepage:

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

License:

MIT + file LICENSE

Recipe:

/bioconductor-diffcyt/meta.yaml

Statistical methods for differential discovery analyses in high-dimensional cytometry data (including flow cytometry, mass cytometry or CyTOF, and oligonucleotide-tagged cytometry), based on a combination of high-resolution clustering and empirical Bayes moderated tests adapted from transcriptomics.

package bioconductor-diffcyt

versions:

1.22.0-0,  1.20.0-0,  1.18.0-0,  1.14.0-0,  1.12.0-0,  1.10.0-1,  1.10.0-0,  1.8.6-0,  1.6.0-0, 

1.22.0-0,  1.20.0-0,  1.18.0-0,  1.14.0-0,  1.12.0-0,  1.10.0-1,  1.10.0-0,  1.8.6-0,  1.6.0-0,  1.4.3-0,  1.2.23-1,  1.2.0-0

depends bioconductor-complexheatmap:

>=2.18.0,<2.19.0

depends bioconductor-edger:

>=4.0.0,<4.1.0

depends bioconductor-flowcore:

>=2.14.0,<2.15.0

depends bioconductor-flowsom:

>=2.10.0,<2.11.0

depends bioconductor-limma:

>=3.58.0,<3.59.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-base:

>=4.3,<4.4.0a0

depends r-circlize:

depends r-dplyr:

depends r-lme4:

depends r-magrittr:

depends r-multcomp:

depends r-reshape2:

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-diffcyt

and update with::

   mamba update bioconductor-diffcyt

To create a new environment, run:

mamba create --name myenvname bioconductor-diffcyt

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-diffcyt:<tag>

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

Download stats

Link to this page

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