Package Recipe 'bioconductor-clusterfoldsimilarity'

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:

1.6.0-0, 1.2.0-0

Depends:

on bioconductor-biocparallel >=1.44.0,<1.45.0
on bioconductor-singlecellexperiment >=1.32.0,<1.33.0
on r-base >=4.5,<4.6.0a0
on r-cowplot
on r-dplyr
on r-ggdendro
on r-ggplot2
on r-igraph
on r-matrix
on r-reshape2
on r-scales
on r-seurat
on r-seuratobject

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-clusterfoldsimilarity

to add into an existing workspace instead, run:

pixi add bioconductor-clusterfoldsimilarity

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-clusterfoldsimilarity

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-clusterfoldsimilarity

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/bioconductor-clusterfoldsimilarity:<tag>

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-clusterfoldsimilarity/README.html)