recipe bioconductor-mastr

Markers Automated Screening Tool in R

Homepage:

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

License:

MIT + file LICENSE

Recipe:

/bioconductor-mastr/meta.yaml

mastR is an R package designed for automated screening of signatures of interest for specific research questions. The package is developed for generating refined lists of signature genes from multiple group comparisons based on the results from edgeR and limma differential expression (DE) analysis workflow. It also takes into account the background noise of tissue-specificity, which is often ignored by other marker generation tools. This package is particularly useful for the identification of group markers in various biological and medical applications, including cancer research and developmental biology.

package bioconductor-mastr

versions:

1.2.0-0,  1.0.0-0

depends bioconductor-annotationdbi:

>=1.64.0,<1.65.0

depends bioconductor-biobase:

>=2.62.0,<2.63.0

depends bioconductor-edger:

>=4.0.0,<4.1.0

depends bioconductor-gseabase:

>=1.64.0,<1.65.0

depends bioconductor-limma:

>=3.58.0,<3.59.0

depends bioconductor-msigdb:

>=1.10.0,<1.11.0

depends bioconductor-org.hs.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 r-base:

>=4.3,<4.4.0a0

depends r-dplyr:

depends r-ggplot2:

depends r-ggpubr:

depends r-matrix:

depends r-patchwork:

depends r-seuratobject:

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-mastr

and update with::

   mamba update bioconductor-mastr

To create a new environment, run:

mamba create --name myenvname bioconductor-mastr

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-mastr:<tag>

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

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Link to this page

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