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:

1.0.0-0

depends bioconductor-biocgenerics:

>=0.52.0,<0.53.0

depends bioconductor-ggtree:

>=3.14.0,<3.15.0

depends bioconductor-scater:

>=1.34.0,<1.35.0

depends bioconductor-singlecellexperiment:

>=1.28.0,<1.29.0

depends r-aplot:

depends r-base:

>=4.4,<4.5.0a0

depends r-cli:

depends r-dplyr:

depends r-ggplot2:

depends r-ggsci:

depends r-magrittr:

depends r-purrr:

depends r-rlang:

depends r-scales:

depends r-seurat:

depends r-stringr:

depends r-tibble:

depends r-tidyr:

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-scdotplot

and update with::

   mamba update bioconductor-scdotplot

To create a new environment, run:

mamba create --name myenvname bioconductor-scdotplot

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-scdotplot:<tag>

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

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Link to this page

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