recipe bioconductor-receptloss

Unsupervised Identification of Genes with Expression Loss in Subsets of Tumors

Homepage:

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

License:

GPL-3 + file LICENSE

Recipe:

/bioconductor-receptloss/meta.yaml

receptLoss identifies genes whose expression is lost in subsets of tumors relative to normal tissue. It is particularly well-suited in cases where the number of normal tissue samples is small, as the distribution of gene expression in normal tissue samples is approximated by a Gaussian. Originally designed for identifying nuclear hormone receptor expression loss but can be applied transcriptome wide as well.

package bioconductor-receptloss

(downloads) docker_bioconductor-receptloss

versions:

1.14.0-0,  1.12.0-0,  1.10.0-0,  1.6.0-0,  1.4.0-0,  1.2.0-1,  1.2.0-0,  1.0.0-0

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-magrittr:

depends r-tidyr:

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-receptloss

and update with::

   mamba update bioconductor-receptloss

To create a new environment, run:

mamba create --name myenvname bioconductor-receptloss

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-receptloss:<tag>

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

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

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