KEGG.db protocols

View KEGG.db computational protocol

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KEGG.db specifications

Information


Unique identifier OMICS_19771
Name KEGG.db
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Version 3.2.3
Stability Stable
Requirements
AnnotationDbi, methods, DBI, R(>=2.7.0), AnnotationDbi(>=1.34.3)
Maintained Yes

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KEGG.db in pipelines

 (2)
2017
PMCID: 5482156
PMID: 28560425
DOI: 10.3892/mmr.2017.6636

[…] expression pattern of those degs was characterized. the resultant heatmaps for the degs were classified as targeted biological processes or kegg pathways using r package., the r packages go.db (), kegg.db () and keggrest () were utilized to detect gene ontology categories and kegg pathways with significant overrepresentation in degs compared with the whole genome. the significantly enriched […]

2016
PMCID: 4938541
PMID: 27391090
DOI: 10.1371/journal.pone.0149640

[…] and the expression pattern of those degs was characterized, and heatmaps for the degs classified in targeted biological processes or kegg pathways using r package., we utilized r packages–go.db, kegg.db and keggrest to detect gene ontology categories and kegg pathways with significant enrichment in degs comparing to which across all measured genes. the significantly enriched biological […]


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KEGG.db in publications

 (45)
PMCID: 5811508
PMID: 29440659
DOI: 10.1038/s41467-017-02772-x

[…] common genes. we then used the heatmap.2 function from gplots to calculate the heatmap with dendrogram in fig. ., for functional enrichment analysis we used the r libraries: dose, clusterprofiler, kegg.db following the tutorial of clusterprofiler., for differential expression analysis we used the statistical methods implemented in the edger package. we started by building a matrix with gene […]

PMCID: 5796182
PMID: 29329273
DOI: 10.3390/ijms19010234

[…] enrichment analysis is a method of cross-integration between biology and mathematics, which is the best choice to solve the massive data of gene chip. in this study, we used the gostats and kegg.db toolkit in the r language to perform functional enrichment analysis on the significantly differentially expressed genes and select the go entry with a count value greater than or equal to 2 […]

PMCID: 5787419
PMID: 29416677
DOI: 10.18632/oncotarget.23148

[…] exposed lower leg (skin), thyroid, and whole blood respectively. we considered these nine tissues in our study. we also obtained the go terms and kegg pathways using r package ‘org.hs.eg.db’ and ‘kegg.db’ (on june 13, 2016). to avoid too general functions, we only used go terms and kegg pathways with less than 500 genes, resulting in 12199 go terms and 279 kegg pathways., it was found […]

PMCID: 5711951
PMID: 29196655
DOI: 10.1038/s41598-017-17114-6

[…] reconstruct the flagella-biofilm regulatory network, information regarding the transcriptional regulation of e. coli was gathered from scientific articles and compiled with that from regulondb and kegg db, and from the extensive analysis of the literature. we used only experimentally validated interaction and not large-scale data or computational predictions. the resulting network consisted […]

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

[…] gene set expression (i.e. enrichment) data between 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 […]


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