bioconductor.org "KEGG" keyword
View the packages on the bioconductor.org package registry that are tagged with the "KEGG" keyword.
mirIntegrator 1.38.0
Integrating microRNA expression into signaling pathways for pathway analysis5 versions - Latest release: 3 months ago - 16.8 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 1.4% on bioconductor.org
5 versions - Latest release: 3 months ago - 49 dependent packages - 1.18 million downloads total - 1 maintainer
GSEABase 1.70.0
Gene set enrichment data structures and methods5 versions - Latest release: 3 months ago - 49 dependent packages - 1.18 million downloads total - 1 maintainer
Top 1.2% on bioconductor.org
14 versions - Latest release: 3 months ago - 59 dependent packages - 1.93 million downloads total - 1 maintainer
clusterProfiler 4.16.0
A universal enrichment tool for interpreting omics data14 versions - Latest release: 3 months ago - 59 dependent packages - 1.93 million downloads total - 1 maintainer
Top 2.7% on bioconductor.org
5 versions - Latest release: 2 months ago - 13 dependent packages - 644 thousand downloads total - 1 maintainer
KEGGgraph 1.68.0
KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor5 versions - Latest release: 2 months ago - 13 dependent packages - 644 thousand downloads total - 1 maintainer
Top 1.9% on bioconductor.org
15 versions - Latest release: 9 days ago - 15 dependent packages - 1.73 million downloads total - 1 maintainer
enrichplot 1.28.4
Visualization of Functional Enrichment Result15 versions - Latest release: 9 days ago - 15 dependent packages - 1.73 million downloads total - 1 maintainer
RegionalST 1.6.0
Investigating regions of interest and performing regional cell type-specific analysis with spatia...6 versions - Latest release: 2 months ago - 3.74 thousand downloads total - 1 maintainer
SVP 1.0.2
Predicting cell states and their variability in single-cell or spatial omics data3 versions - Latest release: 3 days ago - 1.41 thousand downloads total - 9 stars on GitHub - 1 maintainer
MicrobiomeProfiler 1.14.0
An R/shiny package for microbiome functional enrichment analysis5 versions - Latest release: 3 months ago - 8.48 thousand downloads total - 37 stars on GitHub - 1 maintainer
MetaboDynamics 1.0.2
Bayesian analysis of longitudinal metabolomics data2 versions - Latest release: about 1 month ago - 1.59 thousand downloads total - 5 stars on GitHub - 1 maintainer
GeDi 1.4.0
Defining and visualizing the distances between different genesets4 versions - Latest release: 3 months ago - 3.29 thousand downloads total - 1 stars on GitHub - 1 maintainer
FELLA 1.28.0
Interpretation and enrichment for metabolomics data5 versions - Latest release: 3 months ago - 19.5 thousand downloads total - 1 maintainer
DEsubs 1.34.0
DEsubs: an R package for flexible identification of differentially expressed subpathways using RN...5 versions - Latest release: 3 months ago - 15.8 thousand downloads total - 2 maintainers
funOmics 1.2.0
Aggregating Omics Data into Higher-Level Functional Representations2 versions - Latest release: 3 months ago - 2.34 thousand downloads total - 6 stars on GitHub - 1 maintainer
OmnipathR 3.16.0
OmniPath web service client and more7 versions - Latest release: 3 months ago - 3 dependent packages - 44 thousand downloads total - 1 maintainer
PathNet 1.48.0
An R package for pathway analysis using topological information5 versions - Latest release: 3 months ago - 24.9 thousand downloads total - 1 maintainer
Top 7.7% on bioconductor.org
5 versions - Latest release: 3 months ago - 43 thousand downloads total - 2 maintainers
GDCRNATools 1.28.0
GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, mRNA, and miRNA data i...5 versions - Latest release: 3 months ago - 43 thousand downloads total - 2 maintainers
coRdon 1.26.0
Codon Usage Analysis and Prediction of Gene Expressivity5 versions - Latest release: 3 months ago - 19.2 thousand downloads total - 22 stars on GitHub - 1 maintainer
ADAMgui 1.24.0
Activity and Diversity Analysis Module Graphical User Interface5 versions - Latest release: 3 months ago - 12.4 thousand downloads total - 1 maintainer
Top 2.7% on bioconductor.org
5 versions - Latest release: 3 months ago - 5 dependent packages - 251 thousand downloads total - 2 stars on GitHub - 1 maintainer
goseq 1.60.0
Gene Ontology analyser for RNA-seq and other length biased data5 versions - Latest release: 3 months ago - 5 dependent packages - 251 thousand downloads total - 2 stars on GitHub - 1 maintainer
Top 2.7% on bioconductor.org
5 versions - Latest release: 3 months ago - 11 dependent packages - 295 thousand downloads total - 8 stars on GitHub - 1 maintainer
graphite 1.54.0
GRAPH Interaction from pathway Topological Environment5 versions - Latest release: 3 months ago - 11 dependent packages - 295 thousand downloads total - 8 stars on GitHub - 1 maintainer
Top 7.8% on bioconductor.org
5 versions - Latest release: 3 months ago - 1 dependent package - 45.3 thousand downloads total - 1 maintainer
keggorthology 2.60.0
graph support for KO, KEGG Orthology5 versions - Latest release: 3 months ago - 1 dependent package - 45.3 thousand downloads total - 1 maintainer
MetID 1.26.0
Network-based prioritization of putative metabolite IDs5 versions - Latest release: 3 months ago - 9.55 thousand downloads total - 1 stars on GitHub - 1 maintainer
ggkegg 1.6.0
Analyzing and visualizing KEGG information using the grammar of graphics14 versions - Latest release: 3 months ago - 14.4 thousand downloads total - 229 stars on GitHub - 1 maintainer
ginmappeR 1.4.0
Gene Identifier Mapper7 versions - Latest release: 3 months ago - 3.3 thousand downloads total - 1 maintainer
phenomis 1.10.0
Postprocessing and univariate analysis of omics data7 versions - Latest release: 3 months ago - 5.74 thousand downloads total - 1 maintainer
Melissa 1.24.0
Bayesian clustering and imputationa of single cell methylomes5 versions - Latest release: 3 months ago - 9.22 thousand downloads total - 1 maintainer
goSorensen 1.10.0
Statistical inference based on the Sorensen-Dice dissimilarity and the Gene Ontology (GO)5 versions - Latest release: 3 months ago - 5.11 thousand downloads total - 1 maintainer
CTDquerier 2.16.0
Package for CTDbase data query, visualization and downstream analysis5 versions - Latest release: 3 months ago - 9.52 thousand downloads total - 1 maintainer
transomics2cytoscape 1.18.0
A tool set for 3D Trans-Omic network visualization with Cytoscape6 versions - Latest release: 3 months ago - 7.69 thousand downloads total - 1 maintainer
pairkat 1.14.0
PaIRKAT5 versions - Latest release: 3 months ago - 6 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 9.8% on bioconductor.org
6 versions - Latest release: 3 months ago - 1 dependent package - 34.5 thousand downloads total - 1 maintainer
EGSEA 1.36.0
Ensemble of Gene Set Enrichment Analyses6 versions - Latest release: 3 months ago - 1 dependent package - 34.5 thousand downloads total - 1 maintainer
ADAM 1.24.0
ADAM: Activity and Diversity Analysis Module5 versions - Latest release: 3 months ago - 1 dependent package - 13.7 thousand downloads total - 1 maintainer
dce 1.13.0
Pathway Enrichment Based on Differential Causal Effects4 versions - Latest release: 8 months ago - 6.41 thousand downloads total - 13 stars on GitHub - 1 maintainer
UniProt.ws 2.48.0
R Interface to UniProt Web Services5 versions - Latest release: 3 months ago - 6 dependent packages - 66 thousand downloads total - 5 stars on GitHub - 1 maintainer
cogena 1.42.0
co-expressed gene-set enrichment analysis5 versions - Latest release: 3 months ago - 22.5 thousand downloads total - 12 stars on GitHub - 1 maintainer
MetaboSignal 1.38.0
MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathways6 versions - Latest release: 3 months ago - 18.5 thousand downloads total - 2 maintainers
dearseq 1.20.0
Differential Expression Analysis for RNA-seq data through a robust variance component test5 versions - Latest release: 3 months ago - 2 dependent packages - 16 thousand downloads total - 6 stars on GitHub - 1 maintainer
Top 9.0% on bioconductor.org
5 versions - Latest release: 3 months ago - 2 dependent packages - 35.5 thousand downloads total - 1 maintainer
MLP 1.56.0
Mean Log P Analysis5 versions - Latest release: 3 months ago - 2 dependent packages - 35.5 thousand downloads total - 1 maintainer
scBFA 1.22.0
A dimensionality reduction tool using gene detection pattern to mitigate noisy expression profile...5 versions - Latest release: 3 months ago - 9.33 thousand downloads total - 1 maintainer
Top 9.3% on bioconductor.org
5 versions - Latest release: 3 months ago - 1 dependent package - 40.5 thousand downloads total - 1 maintainer
MAGeCKFlute 2.12.0
Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic Screens5 versions - Latest release: 3 months ago - 1 dependent package - 40.5 thousand downloads total - 1 maintainer
signatureSearch 1.22.0
Environment for Gene Expression Searching Combined with Functional Enrichment Analysis5 versions - Latest release: 3 months ago - 16.1 thousand downloads total - 17 stars on GitHub - 1 maintainer
biodb 1.16.0
biodb, a library and a development framework for connecting to chemical and biological databases5 versions - Latest release: 3 months ago - 10 dependent packages - 13.7 thousand downloads total - 11 stars on GitHub - 1 maintainer
CHRONOS 1.36.0
CHRONOS: A time-varying method for microRNA-mediated sub-pathway enrichment analysis5 versions - Latest release: 3 months ago - 16.1 thousand downloads total - 1 maintainer
MetMashR 1.2.0
Metabolite Mashing with R2 versions - Latest release: 3 months ago - 1.21 thousand downloads total - 2 stars on GitHub - 1 maintainer
attract 1.60.0
Methods to Find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor La...5 versions - Latest release: 3 months ago - 36.8 thousand downloads total - 1 maintainer
slalom 1.30.0
Factorial Latent Variable Modeling of Single-Cell RNA-Seq Data5 versions - Latest release: 3 months ago - 13.7 thousand downloads total - 1 maintainer
KEGGlincs 1.34.0
Visualize all edges within a KEGG pathway and overlay LINCS data5 versions - Latest release: 3 months ago - 15.2 thousand downloads total - 2 maintainers
canceR 1.42.0
A Graphical User Interface for accessing and modeling the Cancer Genomics Data of MSKCC8 versions - Latest release: 3 months ago - 23.8 thousand downloads total - 8 stars on GitHub - 1 maintainer
iNETgrate 1.6.0
Integrates DNA methylation data with gene expression in a single gene network4 versions - Latest release: 3 months ago - 4.25 thousand downloads total - 65 stars on GitHub - 1 maintainer
BPRMeth 1.34.0
Model higher-order methylation profiles5 versions - Latest release: 3 months ago - 1 dependent package - 16.4 thousand downloads total - 1 maintainer
VaSP 1.20.0
Quantification and Visualization of Variations of Splicing in Population5 versions - Latest release: 3 months ago - 6.78 thousand downloads total - 3 stars on GitHub - 1 maintainer
famat 1.18.0
Functional analysis of metabolic and transcriptomic data5 versions - Latest release: 2 months ago - 7.09 thousand downloads total - 1 stars on GitHub - 1 maintainer
MetaPhOR 1.10.0
Metabolic Pathway Analysis of RNA5 versions - Latest release: 3 months ago - 5.16 thousand downloads total - 1 maintainer
PanViz 1.10.0
Integrating Multi-Omic Network Data With Summay-Level GWAS Data5 versions - Latest release: 3 months ago - 3.25 thousand downloads total - 3 stars on GitHub - 1 maintainer
fenr 1.6.1
Fast functional enrichment for interactive applications11 versions - Latest release: about 1 month ago - 4.5 thousand downloads total - 0 stars on GitHub - 1 maintainer
paxtoolsr 1.42.0
Access Pathways from Multiple Databases Through BioPAX and Pathway Commons5 versions - Latest release: 2 months ago - 27.3 thousand downloads total - 10 stars on GitHub - 1 maintainer
MIGSA 1.24.0 removed
Massive and Integrative Gene Set Analysis1 version - Latest release: almost 2 years ago - 7.89 thousand downloads total - 0 stars on GitHub - 1 maintainer
RandomWalkRestartMH 1.26.0 removed
Random walk with restart on multiplex and heterogeneous Networks4 versions - Latest release: 8 months ago - 1 dependent package - 10.7 thousand downloads total - 21 stars on GitHub - 1 maintainer
biodbKegg 1.11.0 removed
biodbKegg, a library for connecting to the KEGG Database5 versions - Latest release: 8 months ago - 4.81 thousand downloads total - 2 stars on GitHub - 1 maintainer
Top 1.2% on bioconductor.org
5 versions - Latest release: 9 months ago - 35 dependent packages - 2.85 million downloads total - 1 maintainer
KEGGREST 1.46.0
Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG)5 versions - Latest release: 9 months ago - 35 dependent packages - 2.85 million downloads total - 1 maintainer
PloGO2 1.16.0 removed
Plot Gene Ontology and KEGG pathway Annotation and Abundance3 versions - Latest release: about 1 year ago - 4.86 thousand downloads total - 2 maintainers
StarBioTrek 1.30.0 removed
StarBioTrek3 versions - Latest release: about 1 year ago - 10.4 thousand downloads total - 0 stars on GitHub - 1 maintainer
InterMineR 1.26.0 removed
R Interface with InterMine-Powered Databases4 versions - Latest release: about 1 year ago - 12 thousand downloads total - 17 stars on GitHub - 1 maintainer
ASpediaFI 1.14.0 removed
ASpedia-FI: Functional Interaction Analysis of Alternative Splicing Events1 version - Latest release: almost 2 years ago - 3.82 thousand downloads total - 1 stars on GitHub - 1 maintainer
GRridge 1.26.0 removed
Better prediction by use of co-data: Adaptive group-regularized ridge regression2 versions - Latest release: over 1 year ago - 7.94 thousand downloads total - 1 maintainer
netboxr 1.11.0 removed
netboxr1 version - Latest release: almost 2 years ago - 2.92 thousand downloads total - 1 maintainer
BiocSet 1.18.0
Representing Different Biological Sets4 versions - Latest release: about 1 year ago - 4 dependent packages - 19.4 thousand downloads total - 1 maintainer
Related Keywords
Software
67
Pathways
42
GeneExpression
28
GeneSetEnrichment
27
GO
23
GraphAndNetwork
22
Network
22
Reactome
17
Visualization
16
RNASeq
15
DifferentialExpression
12
ImmunoOncology
12
Clustering
11
SystemsBiology
11
Sequencing
11
Annotation
10
NetworkEnrichment
10
Metabolomics
10
Microarray
9
Transcriptomics
9
MultipleComparison
8
r
7
DataImport
7
Regression
6
SingleCell
6
Genetics
6
GeneRegulation
6
Normalization
5
Proteomics
5
Infrastructure
5
Coverage
5
ThirdPartyClient
5
NetworkInference
5
BiomedicalInformatics
5
Transcription
5
GeneTarget
5
DataRepresentation
4
GenePrediction
4
StatisticalMethod
4
FunctionalPrediction
4
Bayesian
4
DimensionReduction
3
AlternativeSplicing
3
bioinformatics
3
QualityControl
3
DNAMethylation
3
Classification
3
Survival
3
GeneSignaling
3
visualization
2
TimeCourse
2
CellBiology
2
kegg
2
Epigenetics
2
FeatureExtraction
2
WorkflowStep
2
GUI
2
GenomeWideAssociation
2
Spatial
2
SNP
2
BatchEffect
2
BioCarta
2
pathways
2
FunctionalGenomics
2
bioconductor
2
biology
2
gene-sets
1
3s-scores
1
tidygraph
1
alternative-splicing
1
intermine
1
methylation
1
mskcc
1
Preprocessing
1
DifferentialSplicing
1
mutations
1
tcltk
1
PrincipalComponent
1
r-package
1
mRNAMicroarray
1
cran
1
core-services
1
genomics
1
GenomeAnnotation
1
ComparativeGenomics
1
kegg-databases
1
biodb
1
systems-biology
1
networks
1
multiplex-networks
1
computational-biology
1
complex-systems
1
SomaticMutation
1
MathematicalBiology
1
shiny
1
genes
1
gene-ontology
1
compound
1
statistics
1
sqtl
1