recipe bioconductor-easycelltype

Annotate cell types for scRNA-seq data






We developed EasyCellType which can automatically examine the input marker lists obtained from existing software such as Seurat over the cell markerdatabases. Two quantification approaches to annotate cell types are provided: Gene set enrichment analysis (GSEA) and a modified versio of Fisher's exact test. The function presents annotation recommendations in graphical outcomes: bar plots for each cluster showing candidate cell types, as well as a dot plot summarizing the top 5 significant annotations for each cluster.

package bioconductor-easycelltype

(downloads) docker_bioconductor-easycelltype



depends bioconductor-annotationdbi:


depends bioconductor-clusterprofiler:






depends r-base:


depends r-dplyr:

depends r-forcats:

depends r-ggplot2:

depends r-magrittr:

depends r-rlang:



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-easycelltype

and update with::

   mamba update bioconductor-easycelltype

To create a new environment, run:

mamba create --name myenvname bioconductor-easycelltype

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<tag>

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

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