recipe bioconductor-famat

Functional analysis of metabolic and transcriptomic data

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/famat.html

License:

GPL-3

Recipe:

/bioconductor-famat/meta.yaml

Famat is made to collect data about lists of genes and metabolites provided by user, and to visualize it through a Shiny app. Information collected is: - Pathways containing some of the user's genes and metabolites (obtained using a pathway enrichment analysis). - Direct interactions between user's elements inside pathways. - Information about elements (their identifiers and descriptions). - Go terms enrichment analysis performed on user's genes. The Shiny app is composed of: - information about genes, metabolites, and direct interactions between them inside pathways. - an heatmap showing which elements from the list are in pathways (pathways are structured in hierarchies). - hierarchies of enriched go terms using Molecular Function and Biological Process.

package bioconductor-famat

Versions:

1.8.0-0,  1.4.0-0,  1.1.1-0,  1.0.0-1,  1.0.0-0

Depends:

• bioconductor-clusterprofiler >=4.6.0,<4.7.0

• bioconductor-go.db >=3.16.0,<3.17.0

• bioconductor-keggrest >=1.38.0,<1.39.0

• bioconductor-org.hs.eg.db >=3.16.0,<3.17.0

• bioconductor-reactome.db >=1.82.0,<1.83.0

• bioconductor-rwikipathways >=1.18.0,<1.19.0

• r-base >=4.2,<4.3.0a0

• r-biasedurn

• r-dplyr

• r-dt

• r-gprofiler2

• r-magrittr

• r-mgcv

• r-ontologyindex

• r-plotly

• r-shiny

• r-shinybs

• r-shinydashboard

• r-stringr

• r-tidyr

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-famat

and update with:

conda update bioconductor-famat

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-famat:<tag>

(see bioconductor-famat/tags for valid values for <tag>)

Download stats

Link to this page

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