recipe bioconductor-nipalsmcia

Multiple Co-Inertia Analysis via the NIPALS Method

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-nipalsmcia/meta.yaml

Computes Multiple Co-Inertia Analysis (MCIA), a dimensionality reduction (jDR) algorithm, for a multi-block dataset using a modification to the Nonlinear Iterative Partial Least Squares method (NIPALS) proposed in (Hanafi et. al, 2010). Allows multiple options for row- and table-level preprocessing, and speeds up computation of variance explained. Vignettes detail application to bulk- and single cell- multi-omics studies.

package bioconductor-nipalsmcia

versions:

1.0.0-0

depends bioconductor-complexheatmap:

>=2.18.0,<2.19.0

depends bioconductor-fgsea:

>=1.28.0,<1.29.0

depends bioconductor-multiassayexperiment:

>=1.28.0,<1.29.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-base:

>=4.3,<4.4.0a0

depends r-dplyr:

depends r-ggplot2:

>=3.0.0

depends r-pracma:

depends r-rlang:

depends r-rspectra:

depends r-scales:

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-nipalsmcia

and update with::

   mamba update bioconductor-nipalsmcia

To create a new environment, run:

mamba create --name myenvname bioconductor-nipalsmcia

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-nipalsmcia:<tag>

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

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Link to this page

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