KEGGgraph protocols

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KEGGgraph specifications

Information


Unique identifier OMICS_12331
Name KEGGgraph
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.40.0
Stability Stable
Requirements
R(>=2.10.0), methods, KEGG.db, RColorBrewer, utils, RUnit, org.Hs.eg.db, graph, RBGL, Rgraphviz, hgu133plus2.db, XML(>=2.3-0), SPIA
Maintained Yes

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  • person_outline Jitao David Zhang <>

Publication for KEGGgraph

KEGGgraph in pipelines

 (2)
2015
PMCID: 4668955
PMID: 26692761
DOI: 10.4137/BBI.S30884

[…] packages:[1] org.rn.eg.db_3.0.0 rsubread_1.16.1 biocinstaller_1.16.4[4] venndiagram_1.6.9 rcolorbrewer_1.1–2 gplots_2.16.0[7] gagedata_2.3.1 gage_2.16.0 pathview_1.6.0[10] org.hs.eg.db_3.0.0 kegggraph_1.24.0 graph_1.44.1[13] xml_3.98–1.1 edger_3.8.6 limma_3.22.7[16] org.mm.eg.db_3.0.0 rsqlite_1.0.0 dbi_0.3.1[19] annotationdbi_1.28.2 genomeinfodb_1.2.4 iranges_2.0.1[22] s4vectors_0.4.0 […]

2015
PMCID: 4668955
PMID: 26692761
DOI: 10.4137/BBI.S30884

[…] packages:, [1] org.rn.eg.db_3.0.0 rsubread_1.16.1 biocinstaller_1.16.4, [4] venndiagram_1.6.9 rcolorbrewer_1.1–2 gplots_2.16.0, [7] gagedata_2.3.1 gage_2.16.0 pathview_1.6.0, [10] org.hs.eg.db_3.0.0 kegggraph_1.24.0 graph_1.44.1, [13] xml_3.98–1.1 edger_3.8.6 limma_3.22.7, [16] org.mm.eg.db_3.0.0 rsqlite_1.0.0 dbi_0.3.1, [19] annotationdbi_1.28.2 genomeinfodb_1.2.4 iranges_2.0.1, [22] […]


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KEGGgraph in publications

 (32)
PMCID: 5933740
PMID: 29723215
DOI: 10.1371/journal.pone.0196351

[…] geo2r was employed to get the fold change data of individual genes., to obtain the kegg signaling pathways, the “pathview” r package was employed to download kgmls of humans pathways []. then the “kegggraph” r package was used to extract nodes and edges of kegg signaling pathways from kgmls []. in total, 282 signaling pathways were collected from seven categories: metabolism, genetic […]

PMCID: 5703456
PMID: 29176882
DOI: 10.1371/journal.pone.0188071

[…] previously []. briefly, the enrichment of gene ontology (go) [] and kyoto encyclopedia of genes and genomes (kegg) [] pathways was calculated in r by using the bioconductor packages biomart [] and kegggraph []. the background set of proteins for the go analysis involved all constituent proteins from the human ppi network, and we used the complete go tree annotation, excluding the root […]

PMCID: 5680785
PMID: 29121865
DOI: 10.1186/s12864-017-4236-y

[…] different time points (unpaired, q-value <0.1). gene sets were defined using annotations obtained from gage v2.22.0, go.db v3.2.2, and kegg.db v3.2.2. the r package “pathview” v.1.12.0 and kegggraph v1.30.0 were used to visualize gene set expression data in the context of functional pathways [, ]., cummerbund was used to perform k-means clustering (cscluster and csclusterplot […]

PMCID: 5663855
PMID: 29089527
DOI: 10.1038/s41598-017-14650-z

[…] (figures m2–m2). gene identifiers for de genes and background universal lists were converted to entrez ids and kegg pathway analysis was completed on each gene list; results were visualized using kegggraph and pathview. kegg p-values were corrected using hypergeometric testing and significant (q < 0.05) categories are summarised in tables m1 and m2 for methods one and two respectively., […]

PMCID: 5648141
PMID: 29049295
DOI: 10.1371/journal.pone.0186004

[…] eight random topologies from each gene group, resulting in 360 bayesian networks., the methods described in this experiment were performed using the following r packages: rismed [], keggrest [], and kegggraph []. all bayesian and consensus network generation for ds1 was done on the blue waters petascale machine at the university of illinois at urbana-champaign utilizing 1024 cray cpu-only xe6 […]


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KEGGgraph institution(s)
Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
KEGGgraph funding source(s)
National Genome Research Network (grant number 01GS0864) of the German Federal Ministry of Education and Research (BMBF); International PhD program of the DKFZ.

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