How To Install R-biomaRt on Fedora 36

In this tutorial we learn how to install R-biomaRt in Fedora 36. R-biomaRt is R Interface to BioMart databases

Introduction

In this tutorial we learn how to install R-biomaRt on Fedora 36.

What is `R-biomaRt`

In recent years a wealth of biological data has become available in public data repositories. Easy access to these valuable data resources and firm integration with data analysis is needed for comprehensive bioinformatics data analysis. biomaRt provides an interface to a growing collection of databases implementing the BioMart software suite (http enables retrieval of large amounts of data in a uniform way without the need to know the underlying database schemas or write complex SQL queries. Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene, Wormbase and dbSNP mapped to Ensembl. These major databases give biomaRt users direct access to a diverse set of data and enable a wide range of powerful online queries from gene annotation to database mining.

We can use yum or dnf to install R-biomaRt on Fedora 36. In this tutorial we discuss both methods but you only need to choose one of method to install R-biomaRt.

Install R-biomaRt on Fedora 36 Using dnf

Update yum database with dnf using the following command.

sudo dnf makecache --refresh

After updating yum database, We can install R-biomaRt using dnf by running the following command:

sudo dnf -y install R-biomaRt

Install R-biomaRt on Fedora 36 Using yum

Update yum database with yum using the following command.

sudo yum makecache --refresh

After updating yum database, We can install R-biomaRt using yum by running the following command:

sudo yum -y install R-biomaRt

How To Uninstall R-biomaRt on Fedora 36

To uninstall only the R-biomaRt package we can use the following command:

sudo dnf remove R-biomaRt

R-biomaRt Package Contents on Fedora 36

/usr/share/R/library/biomaRt
/usr/share/R/library/biomaRt/CITATION
/usr/share/R/library/biomaRt/DESCRIPTION
/usr/share/R/library/biomaRt/INDEX
/usr/share/R/library/biomaRt/Meta
/usr/share/R/library/biomaRt/Meta/Rd.rds
/usr/share/R/library/biomaRt/Meta/features.rds
/usr/share/R/library/biomaRt/Meta/hsearch.rds
/usr/share/R/library/biomaRt/Meta/links.rds
/usr/share/R/library/biomaRt/Meta/nsInfo.rds
/usr/share/R/library/biomaRt/Meta/package.rds
/usr/share/R/library/biomaRt/Meta/vignette.rds
/usr/share/R/library/biomaRt/NAMESPACE
/usr/share/R/library/biomaRt/NEWS
/usr/share/R/library/biomaRt/R
/usr/share/R/library/biomaRt/R/biomaRt
/usr/share/R/library/biomaRt/R/biomaRt.rdb
/usr/share/R/library/biomaRt/R/biomaRt.rdx
/usr/share/R/library/biomaRt/doc
/usr/share/R/library/biomaRt/doc/accessing_ensembl.R
/usr/share/R/library/biomaRt/doc/accessing_ensembl.Rmd
/usr/share/R/library/biomaRt/doc/accessing_ensembl.html
/usr/share/R/library/biomaRt/doc/accessing_other_marts.R
/usr/share/R/library/biomaRt/doc/accessing_other_marts.Rmd
/usr/share/R/library/biomaRt/doc/accessing_other_marts.html
/usr/share/R/library/biomaRt/doc/index.html
/usr/share/R/library/biomaRt/help
/usr/share/R/library/biomaRt/help/AnIndex
/usr/share/R/library/biomaRt/help/Mart-class.html
/usr/share/R/library/biomaRt/help/NP2009code.html
/usr/share/R/library/biomaRt/help/aliases.rds
/usr/share/R/library/biomaRt/help/attributePages.html
/usr/share/R/library/biomaRt/help/biomaRt-deprecated.html
/usr/share/R/library/biomaRt/help/biomaRt.rdb
/usr/share/R/library/biomaRt/help/biomaRt.rdx
/usr/share/R/library/biomaRt/help/biomartCache.html
/usr/share/R/library/biomaRt/help/biomartCacheClear.html
/usr/share/R/library/biomaRt/help/biomartCacheInfo.html
/usr/share/R/library/biomaRt/help/columns+2CMart-method.html
/usr/share/R/library/biomaRt/help/columns.html
/usr/share/R/library/biomaRt/help/exportFASTA.html
/usr/share/R/library/biomaRt/help/filterOptions.html
/usr/share/R/library/biomaRt/help/filterType.html
/usr/share/R/library/biomaRt/help/getBM.html
/usr/share/R/library/biomaRt/help/getBMlist.html
/usr/share/R/library/biomaRt/help/getGene.html
/usr/share/R/library/biomaRt/help/getLDS.html
/usr/share/R/library/biomaRt/help/getSequence.html
/usr/share/R/library/biomaRt/help/keys+2CMart-method.html
/usr/share/R/library/biomaRt/help/keys.html
/usr/share/R/library/biomaRt/help/keytypes+2CMart-method.html
/usr/share/R/library/biomaRt/help/keytypes.html
/usr/share/R/library/biomaRt/help/listAttributes.html
/usr/share/R/library/biomaRt/help/listDatasets.html
/usr/share/R/library/biomaRt/help/listEnsembl.html
/usr/share/R/library/biomaRt/help/listEnsemblArchives.html
/usr/share/R/library/biomaRt/help/listEnsemblGenomes.html
/usr/share/R/library/biomaRt/help/listFilterOptions.html
/usr/share/R/library/biomaRt/help/listFilterValues.html
/usr/share/R/library/biomaRt/help/listFilters.html
/usr/share/R/library/biomaRt/help/listMarts.html
/usr/share/R/library/biomaRt/help/paths.rds
/usr/share/R/library/biomaRt/help/searchAttributes.html
/usr/share/R/library/biomaRt/help/searchDatasets.html
/usr/share/R/library/biomaRt/help/searchFilterOptions.html
/usr/share/R/library/biomaRt/help/searchFilterValues.html
/usr/share/R/library/biomaRt/help/searchFilters.html
/usr/share/R/library/biomaRt/help/select+2CMart-method.html
/usr/share/R/library/biomaRt/help/select-methods.html
/usr/share/R/library/biomaRt/help/select.html
/usr/share/R/library/biomaRt/help/show+2CMart-method.html
/usr/share/R/library/biomaRt/help/useDataset.html
/usr/share/R/library/biomaRt/help/useEnsembl.html
/usr/share/R/library/biomaRt/help/useEnsemblGenomes.html
/usr/share/R/library/biomaRt/help/useMart.html
/usr/share/R/library/biomaRt/html
/usr/share/R/library/biomaRt/html/00Index.html
/usr/share/R/library/biomaRt/html/Mart-class.html
/usr/share/R/library/biomaRt/html/NP2009code.html
/usr/share/R/library/biomaRt/html/R.css
/usr/share/R/library/biomaRt/html/attributePages.html
/usr/share/R/library/biomaRt/html/biomaRt-deprecated.html
/usr/share/R/library/biomaRt/html/biomartCache.html
/usr/share/R/library/biomaRt/html/exportFASTA.html
/usr/share/R/library/biomaRt/html/filterType.html
/usr/share/R/library/biomaRt/html/getBM.html
/usr/share/R/library/biomaRt/html/getGene.html
/usr/share/R/library/biomaRt/html/getLDS.html
/usr/share/R/library/biomaRt/html/getSequence.html
/usr/share/R/library/biomaRt/html/listAttributes.html
/usr/share/R/library/biomaRt/html/listDatasets.html
/usr/share/R/library/biomaRt/html/listEnsembl.html
/usr/share/R/library/biomaRt/html/listEnsemblArchives.html
/usr/share/R/library/biomaRt/html/listFilterValues.html
/usr/share/R/library/biomaRt/html/listFilters.html
/usr/share/R/library/biomaRt/html/listMarts.html
/usr/share/R/library/biomaRt/html/select.html
/usr/share/R/library/biomaRt/html/useDataset.html
/usr/share/R/library/biomaRt/html/useEnsembl.html
/usr/share/R/library/biomaRt/html/useMart.html
/usr/share/R/library/biomaRt/scripts
/usr/share/R/library/biomaRt/scripts/Integration-NP.R

References

R-biomaRt website

Summary

In this tutorial we learn how to install R-biomaRt on Fedora 36 using yum and [dnf]((/fedora/36/dnf/).