recipe bioconductor-apl

Association Plots

Homepage:

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

License:

GPL (>= 3)

Recipe:

/bioconductor-apl/meta.yaml

APL is a package developed for computation of Association Plots (AP), a method for visualization and analysis of single cell transcriptomics data. The main focus of APL is the identification of genes characteristic for individual clusters of cells from input data. The package performs correspondence analysis (CA) and allows to identify cluster-specific genes using Association Plots. Additionally, APL computes the cluster-specificity scores for all genes which allows to rank the genes by their specificity for a selected cell cluster of interest.

package bioconductor-apl

versions:

1.6.0-0,  1.4.0-0,  1.2.0-0

depends bioconductor-org.hs.eg.db:

>=3.18.0,<3.19.0

depends bioconductor-org.mm.eg.db:

>=3.18.0,<3.19.0

depends bioconductor-singlecellexperiment:

>=1.24.0,<1.25.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends bioconductor-topgo:

>=2.54.0,<2.55.0

depends r-base:

>=4.3,<4.4.0a0

depends r-ggplot2:

depends r-ggrepel:

depends r-magrittr:

depends r-plotly:

depends r-reticulate:

depends r-rlang:

depends r-seurat:

depends r-viridislite:

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-apl

and update with::

   mamba update bioconductor-apl

To create a new environment, run:

mamba create --name myenvname bioconductor-apl

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-apl:<tag>

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

Download stats

Link to this page

Render an badge with the following MarkDown:

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