recipe bioconductor-easycelltype

Annotate cell types for scRNA-seq data

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/EasyCellType.html

License:

Artistic-2.0

Recipe:

/bioconductor-easycelltype/meta.yaml

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

Versions:

1.0.0-0

Depends:

• bioconductor-annotationdbi >=1.60.0,<1.61.0

• bioconductor-clusterprofiler >=4.6.0,<4.7.0

• bioconductor-org.hs.eg.db >=3.16.0,<3.17.0

• bioconductor-org.mm.eg.db >=3.16.0,<3.17.0

• r-base >=4.2,<4.3.0a0

• r-dplyr

• r-forcats

• r-ggplot2

• r-magrittr

• r-rlang

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-easycelltype

and update with:

conda update bioconductor-easycelltype

or use the docker container:

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

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

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