recipe r-swamp

Collection of functions to connect the structure of the data with the information on the samples. Three types of associations are covered: 1. linear model of principal components. 2. hierarchical clustering analysis. 3. distribution of features-sample annotation associations. Additionally, the inter-relation between sample annotations can be analyzed. Simple methods are provided for the correction of batch effects and removal of principal components.

Homepage:

https://CRAN.R-project.org/package=swamp

License:

GPL3 / GPL (>= 2)

Recipe:

/r-swamp/meta.yaml

package r-swamp

(downloads) docker_r-swamp

versions:
1.5.1-5,  1.5.1-4,  1.5.1-3,  1.5.1-2,  1.5.1-1,  1.5.1-0,  1.4.1-3,  1.4.1-2,  1.4.1-1, 

1.5.1-5,  1.5.1-4,  1.5.1-3,  1.5.1-2,  1.5.1-1,  1.5.1-0,  1.4.1-3,  1.4.1-2,  1.4.1-1,  1.4.1-0,  1.3.1-0

depends bioconductor-impute:

depends r-amap:

depends r-base:

>=4.3,<4.4.0a0

depends r-gplots:

depends r-mass:

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 r-swamp

and update with::

   mamba update r-swamp

To create a new environment, run:

mamba create --name myenvname r-swamp

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/r-swamp:<tag>

(see `r-swamp/tags`_ for valid values for ``<tag>``)

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Link to this page

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