recipe bioconductor-scbubbletree

Quantitative visual exploration of scRNA-seq data

Homepage:

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

License:

GPL-3 + file LICENSE

Recipe:

/bioconductor-scbubbletree/meta.yaml

scBubbletree is a quantitative method for visual exploration of scRNA-seq data. It preserves biologically meaningful properties of scRNA-seq data, such as local and global cell distances, as well as the density distribution of cells across the sample. scBubbletree is scalable and avoids the overplotting problem, and is able to visualize diverse cell attributes derived from multiomic single-cell experiments. Importantly, Importantly, scBubbletree is easy to use and to integrate with popular approaches for scRNA-seq data analysis.

package bioconductor-scbubbletree

versions:

1.4.0-0,  1.2.0-0,  1.0.0-0

depends bioconductor-ggtree:

>=3.10.0,<3.11.0

depends r-ape:

depends r-base:

>=4.3,<4.4.0a0

depends r-future:

depends r-future.apply:

depends r-ggplot2:

depends r-patchwork:

depends r-proxy:

depends r-reshape2:

depends r-scales:

depends r-seurat:

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-scbubbletree

and update with::

   mamba update bioconductor-scbubbletree

To create a new environment, run:

mamba create --name myenvname bioconductor-scbubbletree

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-scbubbletree:<tag>

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

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-scbubbletree/README.html)