recipe bioconductor-mistyr

Multiview Intercellular SpaTial modeling framework

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-mistyr/meta.yaml

mistyR is an implementation of the Multiview Intercellular SpaTialmodeling framework (MISTy). MISTy is an explainable machine learning framework for knowledge extraction and analysis of single-cell, highly multiplexed, spatially resolved data. MISTy facilitates an in-depth understanding of marker interactions by profiling the intra- and intercellular relationships. MISTy is a flexible framework able to process a custom number of views. Each of these views can describe a different spatial context, i.e., define a relationship among the observed expressions of the markers, such as intracellular regulation or paracrine regulation, but also, the views can also capture cell-type specific relationships, capture relations between functional footprints or focus on relations between different anatomical regions. Each MISTy view is considered as a potential source of variability in the measured marker expressions. Each MISTy view is then analyzed for its contribution to the total expression of each marker and is explained in terms of the interactions with other measurements that led to the observed contribution.

package bioconductor-mistyr

versions:

1.14.0-0,  1.10.0-0,  1.8.1-0,  1.6.0-0,  1.2.1-0,  1.0.2-0

depends r-assertthat:

depends r-base:

>=4.4,<4.5.0a0

depends r-caret:

depends r-deldir:

depends r-digest:

depends r-distances:

depends r-dplyr:

>=1.1.0

depends r-filelock:

depends r-furrr:

>=0.2.0

depends r-ggplot2:

depends r-purrr:

depends r-r.utils:

depends r-ranger:

depends r-readr:

>=2.0.0

depends r-ridge:

depends r-rlang:

depends r-rlist:

depends r-stringr:

depends r-tibble:

depends r-tidyr:

depends r-tidyselect:

>=1.2.0

depends r-withr:

requirements:

additional platforms:

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-mistyr

and update with::

   mamba update bioconductor-mistyr

To create a new environment, run:

mamba create --name myenvname bioconductor-mistyr

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-mistyr:<tag>

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

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