recipe bioconductor-tissueenrich

Tissue-specific gene enrichment analysis

Homepage:

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

License:

MIT + file LICENSE

Recipe:

/bioconductor-tissueenrich/meta.yaml

The TissueEnrich package is used to calculate enrichment of tissue-specific genes in a set of input genes. For example, the user can input the most highly expressed genes from RNA-Seq data, or gene co-expression modules to determine which tissue-specific genes are enriched in those datasets. Tissue-specific genes were defined by processing RNA-Seq data from the Human Protein Atlas (HPA) (Uhlén et al. 2015), GTEx (Ardlie et al. 2015), and mouse ENCODE (Shen et al. 2012) using the algorithm from the HPA (Uhlén et al. 2015).The hypergeometric test is being used to determine if the tissue-specific genes are enriched among the input genes. Along with tissue-specific gene enrichment, the TissueEnrich package can also be used to define tissue-specific genes from expression datasets provided by the user, which can then be used to calculate tissue-specific gene enrichments.

package bioconductor-tissueenrich

versions:

1.22.0-0,  1.20.0-0,  1.18.0-0,  1.14.0-0,  1.12.0-0,  1.10.0-1,  1.10.0-0,  1.8.0-0,  1.6.0-0, 

1.22.0-0,  1.20.0-0,  1.18.0-0,  1.14.0-0,  1.12.0-0,  1.10.0-1,  1.10.0-0,  1.8.0-0,  1.6.0-0,  1.4.0-1,  1.2.1-0,  1.0.7-0

depends bioconductor-gseabase:

>=1.64.0,<1.65.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-base:

>=4.3,<4.4.0a0

depends r-dplyr:

>=0.7.3

depends r-ensurer:

>=1.1.0

depends r-ggplot2:

>=2.2.1

depends r-tidyr:

>=0.8.0

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-tissueenrich

and update with::

   mamba update bioconductor-tissueenrich

To create a new environment, run:

mamba create --name myenvname bioconductor-tissueenrich

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-tissueenrich:<tag>

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

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Link to this page

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