Package Recipe 'bioconductor-scdotplot'

recipe bioconductor-scdotplot

Cluster a Single-cell RNA-seq Dot Plot

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/scDotPlot.html
License:: Artistic-2.0
Recipe:: /bioconductor-scdotplot/meta.yaml

Dot plots of single-cell RNA-seq data allow for an examination of the relationships between cell groupings (e.g. clusters) and marker gene expression. The scDotPlot package offers a unified approach to perform a hierarchical clustering analysis and add annotations to the columns and/or rows of a scRNA-seq dot plot. It works with SingleCellExperiment and Seurat objects as well as data frames.

package bioconductor-scdotplot¶

Versions:

1.4.0-0, 1.0.0-0

Depends:

on bioconductor-biocgenerics >=0.56.0,<0.57.0
on bioconductor-ggtree >=4.0.0,<4.1.0
on bioconductor-scater >=1.38.0,<1.39.0
on bioconductor-singlecellexperiment >=1.32.0,<1.33.0
on r-aplot
on r-base >=4.5,<4.6.0a0
on r-cli
on r-dplyr
on r-ggplot2
on r-ggsci
on r-magrittr
on r-purrr
on r-rlang
on r-scales
on r-seurat
on r-stringr
on r-tibble
on r-tidyr

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-scdotplot

to add into an existing workspace instead, run:

pixi add bioconductor-scdotplot

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-scdotplot

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-scdotplot

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-scdotplot:<tag>

(see bioconductor-scdotplot/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-scdotplot/README.html)