STRINGdb: STRINGdb (Search Tool for the Retrieval of Interacting proteins database)

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The STRINGdb package provides a R interface to the STRING protein-protein interactions database (http://www.string-db.org).

Author
Andrea Franceschini <andrea.franceschini@isb-sib.ch>
Date of publication
None
Maintainer
Alexander Roth <alexander.roth@isb-sib.ch>
License
GPL-2
Version
1.14.0

View on Bioconductor

Man pages

add_diff_exp_color
add_diff_exp_color
add_proteins_description
add_proteins_description
benchmark_ppi
benchmark_ppi
benchmark_ppi_pathway_view
benchmark_ppi_pathway_view
coeffOfvar
coeffOfvar
delColDf
delColDf
diff_exp_example1
example of microarray data (data processed from GEO GSE9008)
downloadAbsentFile
downloadAbsentFile
downloadAbsentFileSTRING
downloadAbsentFileSTRING
get_aliases
get_aliases
get_annotations
get_annotations
get_annotations_desc
get_annotations_desc
get_bioc_graph
get_bioc_graph
get_clusters
get_clusters
get_enrichment
get_enrichment
get_graph
get_graph
get_homologs
get_homologs
get_homologs_besthits
get_homologs_besthits
get_interactions
get_interactions
get_link
get_link
get_neighbors
get_neighbors
get_png
get_png
get_ppi_enrichment
get_ppi_enrichment
get_ppi_enrichment_full
get_ppi_enrichment_full
get_proteins
get_proteins
get_pubmed
get_pubmed
get_pubmed_interaction
get_pubmed_interaction
get_STRING_species
get_STRING_species
get_subnetwork
get_subnetwork
get_summary
get_summary
get_term_proteins
get_term_proteins
interactions
example of a protein-protein interactions sorted data frame
load
load
load_all
load_all
map
map
mp
mp
multi_map_df
multi_map_df
plot_network
plot_network
plot_ppi_enrichment
plot_ppi_enrichment
plot_ppi_enrichment_graph
plot_ppi_enrichment_graph
post_payload
post_payload
ppie.compLambda
ppie.compLambda
ppie.compLambdaL1L2
ppie.compLambdaL1L2
ppie.compPij
ppie.compPij
ppie.getNumEdgesBetween
ppie.getNumEdgesBetween
ppi_enrichment
ppi_enrichment
ppi_enrichment_full
ppi_enrichment_full
remove_homologous_interactions
remove_homologous_interactions
renameColDf
renameColDf
set_background
set_background
STRINGdb-class
Class '"STRINGdb"'

Files in this package

STRINGdb/DESCRIPTION
STRINGdb/NAMESPACE
STRINGdb/R
STRINGdb/R/ppi_enrichment.R
STRINGdb/R/r_utils.R
STRINGdb/R/rstring.R
STRINGdb/build
STRINGdb/build/vignette.rds
STRINGdb/data
STRINGdb/data/diff_exp_example1.rda
STRINGdb/data/interactions_example.rda
STRINGdb/inst
STRINGdb/inst/CITATION
STRINGdb/inst/doc
STRINGdb/inst/doc/STRINGdb.R
STRINGdb/inst/doc/STRINGdb.Rnw
STRINGdb/inst/doc/STRINGdb.pdf
STRINGdb/inst/unitTests
STRINGdb/inst/unitTests/test_get_homologs.R
STRINGdb/inst/unitTests/test_get_homologs_besthits.R
STRINGdb/inst/unitTests/test_get_pubmed_interaction.R
STRINGdb/man
STRINGdb/man/STRINGdb-class.Rd
STRINGdb/man/add_diff_exp_color.Rd
STRINGdb/man/add_proteins_description.Rd
STRINGdb/man/benchmark_ppi.Rd
STRINGdb/man/benchmark_ppi_pathway_view.Rd
STRINGdb/man/coeffOfvar.Rd
STRINGdb/man/delColDf.Rd
STRINGdb/man/diff_exp_example1.Rd
STRINGdb/man/downloadAbsentFile.Rd
STRINGdb/man/downloadAbsentFileSTRING.Rd
STRINGdb/man/get_STRING_species.Rd
STRINGdb/man/get_aliases.Rd
STRINGdb/man/get_annotations.Rd
STRINGdb/man/get_annotations_desc.Rd
STRINGdb/man/get_bioc_graph.Rd
STRINGdb/man/get_clusters.Rd
STRINGdb/man/get_enrichment.Rd
STRINGdb/man/get_graph.Rd
STRINGdb/man/get_homologs.Rd
STRINGdb/man/get_homologs_besthits.Rd
STRINGdb/man/get_interactions.Rd
STRINGdb/man/get_link.Rd
STRINGdb/man/get_neighbors.Rd
STRINGdb/man/get_png.Rd
STRINGdb/man/get_ppi_enrichment.Rd
STRINGdb/man/get_ppi_enrichment_full.Rd
STRINGdb/man/get_proteins.Rd
STRINGdb/man/get_pubmed.Rd
STRINGdb/man/get_pubmed_interaction.Rd
STRINGdb/man/get_subnetwork.Rd
STRINGdb/man/get_summary.Rd
STRINGdb/man/get_term_proteins.Rd
STRINGdb/man/interactions.Rd
STRINGdb/man/load.Rd
STRINGdb/man/load_all.Rd
STRINGdb/man/map.Rd
STRINGdb/man/mp.Rd
STRINGdb/man/multi_map_df.Rd
STRINGdb/man/plot_network.Rd
STRINGdb/man/plot_ppi_enrichment.Rd
STRINGdb/man/plot_ppi_enrichment_graph.Rd
STRINGdb/man/post_payload.Rd
STRINGdb/man/ppi_enrichment.Rd
STRINGdb/man/ppi_enrichment_full.Rd
STRINGdb/man/ppie.compLambda.Rd
STRINGdb/man/ppie.compLambdaL1L2.Rd
STRINGdb/man/ppie.compPij.Rd
STRINGdb/man/ppie.getNumEdgesBetween.Rd
STRINGdb/man/remove_homologous_interactions.Rd
STRINGdb/man/renameColDf.Rd
STRINGdb/man/set_background.Rd
STRINGdb/tests
STRINGdb/tests/runTests.R
STRINGdb/vignettes
STRINGdb/vignettes/STRINGdb.Rnw
STRINGdb/vignettes/heatmap_enrichment_example.pdf