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The R package STRINGdb provides a convenient interface to the STRING protein-protein interactions database for the R/bioconductor users. Please look at the manual/vignette to get additional informationd and examples on how to use the package. STRING is a database of known and predicted protein-protein interactions. It contains information from numerous sources, including experimental repositories, computational prediction methods and public text collections. Each interaction is associated with a combined confidence score that integrates the various evidences. STRING is regularly updated , the latest version 9.05 contains information on 5 millions proteins from more than 1100 species. The STRING web interface is freely accessible at: http://string-db.org/
● Data Source:
BioConductor
● Keywords: classes
● Alias: STRINGdb, STRINGdb-class
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Take in input a dataframe containing a logFC column that reports the logarithm of the difference in expression level. Add a "color" column to the data frame such that strongly downregulated genes are colored in green and strong upregulated genes are in red. When the down or up-regulation is instead weak the intensity of the color gets weaker as well, accordingly.
● Data Source:
BioConductor
● Keywords:
● Alias: S4method{add_diff_exp_color
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Add description coluns to the proteins that are present in the data frame given in input. The data frame must contain a column named "STRING_id".
● Data Source:
BioConductor
● Keywords:
● Alias: S4method{add_proteins_description
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benchmark a list of protein-protein interactions using pathways (e.g. KEGG). The function outputs a table where the interactions are mapped to KEGG and the number of TPs and FPs are counted.
● Data Source:
BioConductor
● Keywords:
● Alias: S4method{benchmark_ppi
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Takes in input the results of the benchmark_ppi function, and constructs a new table that provides a view at the pathway level (i.e. it list all the pathways to which the interactions belong)
● Data Source:
BioConductor
● Keywords:
● Alias: S4method{benchmark_ppi_pathway_view
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coefficient of variation
● Data Source:
BioConductor
● Keywords:
● Alias: coeffOfvar
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delete a column in the data frame
● Data Source:
BioConductor
● Keywords:
● Alias: delColDf
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download a file only if it is not present.
● Data Source:
BioConductor
● Keywords:
● Alias: downloadAbsentFile
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download a STRING file only if it is not present or if it is corrupted.
● Data Source:
BioConductor
● Keywords:
● Alias: downloadAbsentFileSTRING
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Returns a data frame with the species (i.e. organisms) that are present in STRING.
● Data Source:
BioConductor
● Keywords:
● Alias: get_STRING_species
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providing 
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