recipe bioconductor-goexpress

Visualise microarray and RNAseq data using gene ontology annotations

Homepage:

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

License:

GPL (>= 3)

Recipe:

/bioconductor-goexpress/meta.yaml

The package contains methods to visualise the expression profile of genes from a microarray or RNA-seq experiment, and offers a supervised clustering approach to identify GO terms containing genes with expression levels that best classify two or more predefined groups of samples. Annotations for the genes present in the expression dataset may be obtained from Ensembl through the biomaRt package, if not provided by the user. The default random forest framework is used to evaluate the capacity of each gene to cluster samples according to the factor of interest. Finally, GO terms are scored by averaging the rank (alternatively, score) of their respective gene sets to cluster the samples. P-values may be computed to assess the significance of GO term ranking. Visualisation function include gene expression profile, gene ontology-based heatmaps, and hierarchical clustering of experimental samples using gene expression data.

package bioconductor-goexpress

versions:

1.40.0-0,  1.36.0-0,  1.34.0-0,  1.32.0-0,  1.28.0-0,  1.26.0-0,  1.24.0-1,  1.24.0-0,  1.22.0-0, 

1.40.0-0,  1.36.0-0,  1.34.0-0,  1.32.0-0,  1.28.0-0,  1.26.0-0,  1.24.0-1,  1.24.0-0,  1.22.0-0,  1.20.0-0,  1.18.0-1,  1.16.0-0

depends bioconductor-biobase:

>=2.66.0,<2.67.0

depends bioconductor-biomart:

>=2.62.0,<2.63.0

depends r-base:

>=4.4,<4.5.0a0

depends r-ggplot2:

>=0.9.0

depends r-gplots:

>=2.13.0

depends r-randomforest:

>=4.6

depends r-rcolorbrewer:

>=1.0

depends r-rcurl:

>=1.95

depends r-stringr:

>=0.6.2

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-goexpress

and update with::

   mamba update bioconductor-goexpress

To create a new environment, run:

mamba create --name myenvname bioconductor-goexpress

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-goexpress:<tag>

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

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