recipe bioconductor-mineica

Analysis of an ICA decomposition obtained on genomics data

Homepage:

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

License:

GPL-2

Recipe:

/bioconductor-mineica/meta.yaml

Links:

biotools: mineica, doi: 10.1155/2014/213656

The goal of MineICA is to perform Independent Component Analysis (ICA) on multiple transcriptome datasets, integrating additional data (e.g molecular, clinical and pathological). This Integrative ICA helps the biological interpretation of the components by studying their association with variables (e.g sample annotations) and gene sets, and enables the comparison of components from different datasets using correlation-based graph.

package bioconductor-mineica

versions:

1.42.0-0,  1.40.0-0,  1.38.0-0,  1.34.0-0,  1.32.0-0,  1.30.0-1,  1.30.0-0,  1.28.0-0,  1.26.0-0, 

1.42.0-0,  1.40.0-0,  1.38.0-0,  1.34.0-0,  1.32.0-0,  1.30.0-1,  1.30.0-0,  1.28.0-0,  1.26.0-0,  1.24.0-1,  1.22.0-0,  1.18.0-0

depends bioconductor-annotate:

>=1.80.0,<1.81.0

depends bioconductor-annotationdbi:

>=1.64.0,<1.65.0

depends bioconductor-biobase:

>=2.62.0,<2.63.0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-biomart:

>=2.58.0,<2.59.0

depends bioconductor-gostats:

>=2.68.0,<2.69.0

depends bioconductor-graph:

>=1.80.0,<1.81.0

depends bioconductor-lumi:

>=2.54.0,<2.55.0

depends bioconductor-lumihumanall.db:

>=1.22.0,<1.23.0

depends bioconductor-marray:

>=1.80.0,<1.81.0

depends bioconductor-rgraphviz:

>=2.46.0,<2.47.0

depends r-base:

>=4.3,<4.4.0a0

depends r-cluster:

depends r-colorspace:

depends r-fastica:

depends r-foreach:

depends r-fpc:

depends r-ggplot2:

depends r-gtools:

depends r-hmisc:

depends r-igraph:

depends r-jade:

depends r-mclust:

depends r-plyr:

depends r-rcolorbrewer:

depends r-scales:

depends r-xtable:

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-mineica

and update with::

   mamba update bioconductor-mineica

To create a new environment, run:

mamba create --name myenvname bioconductor-mineica

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-mineica:<tag>

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

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