recipe bioconductor-ctexplorer

Explores Cancer Testis Genes

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/CTexploreR.html

License:

Artistic-2.0

Recipe:

/bioconductor-ctexplorer/meta.yaml

The CTexploreR package re-defines the list of Cancer Testis/Germline (CT) genes. It is based on publicly available RNAseq databases (GTEx, CCLE and TCGA) and summarises CT genes' main characteristics. Several visualisation functions allow to explore their expression in different types of tissues and cancer cells, or to inspect the methylation status of their promoters in normal tissues.

package bioconductor-ctexplorer

versions:

1.2.0-0

depends bioconductor-biocgenerics:

>=0.52.0,<0.53.0

depends bioconductor-complexheatmap:

>=2.22.0,<2.23.0

depends bioconductor-ctdata:

>=1.6.0,<1.7.0

depends bioconductor-genomicranges:

>=1.58.0,<1.59.0

depends bioconductor-iranges:

>=2.40.0,<2.41.0

depends bioconductor-matrixgenerics:

>=1.18.0,<1.19.0

depends bioconductor-singlecellexperiment:

>=1.28.0,<1.29.0

depends bioconductor-summarizedexperiment:

>=1.36.0,<1.37.0

depends r-base:

>=4.4,<4.5.0a0

depends r-circlize:

depends r-dplyr:

depends r-ggplot2:

depends r-ggrepel:

depends r-rlang:

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-ctexplorer

and update with::

   mamba update bioconductor-ctexplorer

To create a new environment, run:

mamba create --name myenvname bioconductor-ctexplorer

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-ctexplorer:<tag>

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

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