recipe bioconductor-viseago

ViSEAGO: a Bioconductor package for clustering biological functions using Gene Ontology and semantic similarity

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-viseago/meta.yaml

The main objective of ViSEAGO package is to carry out a data mining of biological functions and establish links between genes involved in the study. We developed ViSEAGO in R to facilitate functional Gene Ontology (GO) analysis of complex experimental design with multiple comparisons of interest. It allows to study large-scale datasets together and visualize GO profiles to capture biological knowledge. The acronym stands for three major concepts of the analysis: Visualization, Semantic similarity and Enrichment Analysis of Gene Ontology. It provides access to the last current GO annotations, which are retrieved from one of NCBI EntrezGene, Ensembl or Uniprot databases for several species. Using available R packages and novel developments, ViSEAGO extends classical functional GO analysis to focus on functional coherence by aggregating closely related biological themes while studying multiple datasets at once. It provides both a synthetic and detailed view using interactive functionalities respecting the GO graph structure and ensuring functional coherence supplied by semantic similarity. ViSEAGO has been successfully applied on several datasets from different species with a variety of biological questions. Results can be easily shared between bioinformaticians and biologists, enhancing reporting capabilities while maintaining reproducibility.

package bioconductor-viseago

versions:

1.16.0-0,  1.14.0-0,  1.12.0-0,  1.8.0-0,  1.6.0-0,  1.4.0-1,  1.4.0-0,  1.2.0-0,  1.0.0-0

depends bioconductor-annotationdbi:

>=1.64.0,<1.65.0

depends bioconductor-annotationforge:

>=1.44.0,<1.45.0

depends bioconductor-biomart:

>=2.58.0,<2.59.0

depends bioconductor-fgsea:

>=1.28.0,<1.29.0

depends bioconductor-go.db:

>=3.18.0,<3.19.0

depends bioconductor-gosemsim:

>=2.28.0,<2.29.0

depends bioconductor-topgo:

>=2.54.0,<2.55.0

depends r-base:

>=4.3,<4.4.0a0

depends r-data.table:

depends r-dendextend:

depends r-diagrammer:

depends r-dt:

depends r-dynamictreecut:

depends r-ggplot2:

depends r-heatmaply:

depends r-htmlwidgets:

depends r-igraph:

depends r-plotly:

depends r-processx:

depends r-r.utils:

depends r-rcolorbrewer:

depends r-scales:

depends r-upsetr:

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-viseago

and update with::

   mamba update bioconductor-viseago

To create a new environment, run:

mamba create --name myenvname bioconductor-viseago

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-viseago:<tag>

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

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