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

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

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("STRINGdb")
AuthorAndrea Franceschini <andrea.franceschini@isb-sib.ch>
Bioconductor views Network
Date of publicationNone
MaintainerAlexander Roth <alexander.roth@isb-sib.ch>
LicenseGPL-2
Version1.16.0

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"'

Functions

coeffOfvar Man page
delColDf Man page
diff_exp_example1 Man page
downloadAbsentFile Man page
downloadAbsentFileSTRING Man page
get_STRING_species Man page
interactions_example Man page
multi_map_df Man page
plot_ppi_enrichment_graph Man page
ppie.compLambda Man page
ppie.compLambdaL1L2 Man page
ppie.compPij Man page
ppie.getNumEdgesBetween Man page
ppi_enrichment Man page
ppi_enrichment_full Man page
renameColDf Man page
\S4method{add_diff_exp_color}{STRINGdb} Man page
\S4method{add_proteins_description}{STRINGdb} Man page
\S4method{benchmark_ppi_pathway_view}{STRINGdb} Man page
\S4method{benchmark_ppi}{STRINGdb} Man page
\S4method{get_aliases}{STRINGdb} Man page
\S4method{get_annotations_desc}{STRINGdb} Man page
\S4method{get_annotations}{STRINGdb} Man page
\S4method{get_bioc_graph}{STRINGdb} Man page
\S4method{get_clusters}{STRINGdb} Man page
\S4method{get_enrichment}{STRINGdb} Man page
\S4method{get_graph}{STRINGdb} Man page
\S4method{get_homologs_besthits}{STRINGdb} Man page
\S4method{get_homologs}{STRINGdb} Man page
\S4method{get_interactions}{STRINGdb} Man page
\S4method{get_link}{STRINGdb} Man page
\S4method{get_neighbors}{STRINGdb} Man page
\S4method{get_png}{STRINGdb} Man page
\S4method{get_ppi_enrichment_full}{STRINGdb} Man page
\S4method{get_ppi_enrichment}{STRINGdb} Man page
\S4method{get_proteins}{STRINGdb} Man page
\S4method{get_pubmed_interaction}{STRINGdb} Man page
\S4method{get_pubmed}{STRINGdb} Man page
\S4method{get_subnetwork}{STRINGdb} Man page
\S4method{get_summary}{STRINGdb} Man page
\S4method{get_term_proteins}{STRINGdb} Man page
\S4method{load_all}{STRINGdb} Man page
\S4method{load}{STRINGdb} Man page
\S4method{map}{STRINGdb} Man page
\S4method{mp}{STRINGdb} Man page
\S4method{plot_network}{STRINGdb} Man page
\S4method{plot_ppi_enrichment}{STRINGdb} Man page
\S4method{post_payload}{STRINGdb} Man page
\S4method{remove_homologous_interactions}{STRINGdb} Man page
\S4method{set_background}{STRINGdb} Man page
STRINGdb Man page
STRINGdb-class Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.