recipe bioconductor-clusterfoldsimilarity

Calculate similarity of clusters from different single cell samples using foldchanges

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/ClusterFoldSimilarity.html

License:

Artistic-2.0

Recipe:

/bioconductor-clusterfoldsimilarity/meta.yaml

This package calculates a similarity coefficient using the fold changes of shared features (e.g. genes) among clusters of different samples/batches/datasets. The similarity coefficient is calculated using the dot-product (Hadamard product) of every pairwise combination of Fold Changes between a source cluster i of sample/dataset n and all the target clusters j in sample/dataset m

package bioconductor-clusterfoldsimilarity

versions:

1.2.0-0

depends bioconductor-biocparallel:

>=1.40.0,<1.41.0

depends bioconductor-singlecellexperiment:

>=1.28.0,<1.29.0

depends r-base:

>=4.4,<4.5.0a0

depends r-cowplot:

depends r-dplyr:

depends r-ggdendro:

depends r-ggplot2:

depends r-igraph:

depends r-matrix:

depends r-reshape2:

depends r-scales:

depends r-seurat:

depends r-seuratobject:

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-clusterfoldsimilarity

and update with::

   mamba update bioconductor-clusterfoldsimilarity

To create a new environment, run:

mamba create --name myenvname bioconductor-clusterfoldsimilarity

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-clusterfoldsimilarity:<tag>

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

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Link to this page

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