bioconductor.org "KEGG" keyword
coRdon 1.30.0
Codon Usage Analysis and Prediction of Gene Expressivity7 versions - Latest release: 6 months ago - 41.9 thousand downloads total - 22 stars on GitHub - 1 maintainer
OmnipathR 4.0.0
OmniPath web service client and more13 versions - Latest release: 5 months ago - 3 dependent packages - 106 thousand downloads total - 175 stars on GitHub - 1 maintainer
scGraphVerse 1.2.0
scGraphVerse: A Gene Network Analysis Package2 versions - Latest release: 6 months ago - 8.3 thousand downloads total - 2 stars on GitHub - 1 maintainer
DEsubs 1.38.0
DEsubs: an R package for flexible identification of differentially expressed subpathways using RN...7 versions - Latest release: 6 months ago - 36.9 thousand downloads total - 2 maintainers
CTDquerier 2.20.0
Package for CTDbase data query, visualization and downstream analysis7 versions - Latest release: 5 months ago - 30.1 thousand downloads total - 1 maintainer
ADAM 1.28.0
ADAM: Activity and Diversity Analysis Module7 versions - Latest release: 6 months ago - 1 dependent package - 28.8 thousand downloads total - 1 maintainer
Top 1.4% on bioconductor.org
8 versions - Latest release: 6 months ago - 49 dependent packages - 1.57 million downloads total - 1 maintainer
GSEABase 1.74.0
Gene set enrichment data structures and methods8 versions - Latest release: 6 months ago - 49 dependent packages - 1.57 million downloads total - 1 maintainer
transomics2cytoscape 1.22.0
A tool set for 3D Trans-Omic network visualization with Cytoscape8 versions - Latest release: 5 months ago - 21 thousand downloads total - 1 maintainer
slalom 1.34.0
Factorial Latent Variable Modeling of Single-Cell RNA-Seq Data7 versions - Latest release: 6 months ago - 24.4 thousand downloads total - 1 maintainer
canceR 1.46.0
A Graphical User Interface for accessing and modeling the Cancer Genomics Data of MSKCC10 versions - Latest release: 6 months ago - 39.9 thousand downloads total - 8 stars on GitHub - 1 maintainer
RegionalST 1.10.0
Investigating regions of interest and performing regional cell type-specific analysis with spatia...8 versions - Latest release: 5 months ago - 17.4 thousand downloads total - 1 maintainer
Top 1.2% on bioconductor.org
21 versions - Latest release: 9 days ago - 59 dependent packages - 2.92 million downloads total - 1 maintainer
clusterProfiler 4.20.3
A Universal Enrichment Tool for Interpreting Omics Data21 versions - Latest release: 9 days ago - 59 dependent packages - 2.92 million downloads total - 1 maintainer
Top 1.2% on bioconductor.org
6 versions - Latest release: 3 months ago - 35 dependent packages - 5.52 million downloads total - 1 maintainer
KEGGREST 1.52.2
Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG)6 versions - Latest release: 3 months ago - 35 dependent packages - 5.52 million downloads total - 1 maintainer
KEGGlincs 1.38.0
Visualize all edges within a KEGG pathway and overlay LINCS data7 versions - Latest release: 5 months ago - 33.7 thousand downloads total - 2 maintainers
Top 9.8% on bioconductor.org
8 versions - Latest release: 6 months ago - 1 dependent package - 58.5 thousand downloads total - 1 maintainer
EGSEA 1.40.0
Ensemble of Gene Set Enrichment Analyses8 versions - Latest release: 6 months ago - 1 dependent package - 58.5 thousand downloads total - 1 maintainer
MetaboSignal 1.42.1
MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathways9 versions - Latest release: 3 months ago - 40.1 thousand downloads total - 2 maintainers
phenomis 1.14.0
Postprocessing and univariate analysis of omics data9 versions - Latest release: 5 months ago - 16.9 thousand downloads total - 1 maintainer
Top 1.9% on bioconductor.org
23 versions - Latest release: 23 days ago - 15 dependent packages - 2.8 million downloads total - 1 maintainer
enrichplot 1.32.1
Visualization of Functional Enrichment Result23 versions - Latest release: 23 days ago - 15 dependent packages - 2.8 million downloads total - 1 maintainer
BPRMeth 1.38.0
Model higher-order methylation profiles7 versions - Latest release: 6 months ago - 1 dependent package - 28.7 thousand downloads total - 1 maintainer
FELLA 1.32.0
Interpretation and enrichment for metabolomics data7 versions - Latest release: 5 months ago - 1 maintainer
MetMashR 1.6.0
Metabolite Mashing with R5 versions - Latest release: 5 months ago - 12.4 thousand downloads total - 3 stars on GitHub - 1 maintainer
PathNet 1.52.0
An R package for pathway analysis using topological information7 versions - Latest release: 6 months ago - 38.4 thousand downloads total - 1 maintainer
GeDi 1.7.1
Defining and visualizing the distances between different genesets7 versions - Latest release: 6 months ago - 11.9 thousand downloads total - 3 stars on GitHub - 1 maintainer
MetaboDynamics 2.2.1
Bayesian analysis of longitudinal metabolomics data6 versions - Latest release: about 2 months ago - 11.9 thousand downloads total - 5 stars on GitHub - 1 maintainer
Melissa 1.28.0
Bayesian clustering and imputationa of single cell methylomes9 versions - Latest release: 5 months ago - 18.4 thousand downloads total - 1 maintainer
ginmappeR 1.8.0
Gene Identifier Mapper9 versions - Latest release: 6 months ago - 12.1 thousand downloads total - 1 maintainer
goSorensen 1.14.0
Statistical inference based on the Sorensen-Dice dissimilarity and the Gene Ontology (GO)7 versions - Latest release: 6 months ago - 10.3 thousand downloads total - 1 maintainer
ggkegg 1.10.0
Analyzing and visualizing KEGG information using the grammar of graphics17 versions - Latest release: 6 months ago - 29.7 thousand downloads total - 247 stars on GitHub - 1 maintainer
CHRONOS 1.40.0
CHRONOS: A time-varying method for microRNA-mediated sub-pathway enrichment analysis7 versions - Latest release: 6 months ago - 24.4 thousand downloads total - 1 maintainer
SVP 1.4.1
Predicting cell states and their variability in single-cell or spatial omics data6 versions - Latest release: 2 months ago - 7.76 thousand downloads total - 12 stars on GitHub - 1 maintainer
attract 1.64.0
Methods to Find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor La...7 versions - Latest release: 5 months ago - 50 thousand downloads total - 1 maintainer
scBFA 1.26.0
A dimensionality reduction tool using gene detection pattern to mitigate noisy expression profile...7 versions - Latest release: 6 months ago - 17.9 thousand downloads total - 1 maintainer
MicrobiomeProfiler 1.18.1
An R/shiny package for microbiome functional enrichment analysis7 versions - Latest release: 5 months ago - 19.5 thousand downloads total - 42 stars on GitHub - 1 maintainer
RandomWalkRestartMH 1.26.0 removed
Random walk with restart on multiplex and heterogeneous Networks4 versions - Latest release: almost 2 years ago - 1 dependent package - 10.7 thousand downloads total - 23 stars on GitHub - 1 maintainer
Top 2.7% on bioconductor.org
7 versions - Latest release: 6 months ago - 11 dependent packages - 459 thousand downloads total - 8 stars on GitHub - 1 maintainer
graphite 1.58.0
GRAPH Interaction from pathway Topological Environment7 versions - Latest release: 6 months ago - 11 dependent packages - 459 thousand downloads total - 8 stars on GitHub - 1 maintainer
biodb 1.20.0
Biodb, a Library and a Development Framework for Connecting to Chemical and Biological Databases8 versions - Latest release: 6 months ago - 10 dependent packages - 23 thousand downloads total - 0 stars on gitlab.com - 1 maintainer
mirIntegrator 1.42.0
Integrating microRNA expression into signaling pathways for pathway analysis7 versions - Latest release: 6 months ago - 26.6 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 7.7% on bioconductor.org
7 versions - Latest release: 6 months ago - 56.6 thousand downloads total - 2 maintainers
GDCRNATools 1.32.0
GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, mRNA, and miRNA data i...7 versions - Latest release: 6 months ago - 56.6 thousand downloads total - 2 maintainers
famat 1.22.0
Functional analysis of metabolic and transcriptomic data8 versions - Latest release: 5 months ago - 15 thousand downloads total - 1 stars on GitHub - 1 maintainer
pairkat 1.18.0
PaIRKAT7 versions - Latest release: 6 months ago - 13.6 thousand downloads total - 0 stars on GitHub - 1 maintainer
cogena 1.46.0
co-expressed gene-set enrichment analysis7 versions - Latest release: 6 months ago - 33.5 thousand downloads total - 13 stars on GitHub - 1 maintainer
Top 2.7% on bioconductor.org
7 versions - Latest release: 5 months ago - 13 dependent packages - 824 thousand downloads total - 1 maintainer
KEGGgraph 1.72.0
KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor7 versions - Latest release: 5 months ago - 13 dependent packages - 824 thousand downloads total - 1 maintainer
dearseq 1.24.0
Differential Expression Analysis for RNA-seq data through a robust variance component test7 versions - Latest release: 6 months ago - 2 dependent packages - 26.7 thousand downloads total - 6 stars on GitHub - 1 maintainer
funOmics 1.6.0
Aggregating Omics Data into Higher-Level Functional Representations4 versions - Latest release: 5 months ago - 6.97 thousand downloads total - 7 stars on GitHub - 1 maintainer
UniProt.ws 2.52.1
R Interface to UniProt Web Services9 versions - Latest release: 2 months ago - 6 dependent packages - 92.6 thousand downloads total - 10 stars on GitHub - 1 maintainer
Top 2.7% on bioconductor.org
7 versions - Latest release: 6 months ago - 5 dependent packages - 325 thousand downloads total - 2 stars on GitHub - 1 maintainer
goseq 1.64.0
Gene Ontology analyser for RNA-seq and other length biased data7 versions - Latest release: 6 months ago - 5 dependent packages - 325 thousand downloads total - 2 stars on GitHub - 1 maintainer
MetID 1.30.0
Network-based prioritization of putative metabolite IDs7 versions - Latest release: 6 months ago - 16.4 thousand downloads total - 1 stars on GitHub - 1 maintainer
MetaPhOR 1.14.0
Metabolic Pathway Analysis of RNA7 versions - Latest release: 5 months ago - 12.2 thousand downloads total - 1 maintainer
BiocSet 1.25.0
Representing Different Biological Sets5 versions - Latest release: 3 months ago - 4 dependent packages - 45.3 thousand downloads total - 1 maintainer
Top 7.8% on bioconductor.org
7 versions - Latest release: 6 months ago - 1 dependent package - 69.6 thousand downloads total - 1 maintainer
keggorthology 2.64.0
graph support for KO, KEGG Orthology7 versions - Latest release: 6 months ago - 1 dependent package - 69.6 thousand downloads total - 1 maintainer
iNETgrate 1.10.0
Integrates DNA methylation data with gene expression in a single gene network7 versions - Latest release: 6 months ago - 16.1 thousand downloads total - 65 stars on GitHub - 1 maintainer
Top 9.0% on bioconductor.org
7 versions - Latest release: 6 months ago - 2 dependent packages - 55.5 thousand downloads total - 1 maintainer
MLP 1.60.0
Mean Log P Analysis7 versions - Latest release: 6 months ago - 2 dependent packages - 55.5 thousand downloads total - 1 maintainer
VaSP 1.24.0
Quantification and Visualization of Variations of Splicing in Population7 versions - Latest release: 6 months ago - 21.6 thousand downloads total - 3 stars on GitHub - 1 maintainer
fenr 1.10.3
Fast functional enrichment for interactive applications18 versions - Latest release: about 1 month ago - 16.8 thousand downloads total - 0 stars on GitHub - 1 maintainer
anansi 1.2.0
Annotation-Based Analysis of Specific Interactions2 versions - Latest release: 5 months ago - 8.76 thousand downloads total - 11 stars on GitHub - 1 maintainer
StarBioTrek 1.30.0 removed
StarBioTrek3 versions - Latest release: over 2 years ago - 10.4 thousand downloads total - 0 stars on GitHub - 1 maintainer
ADAMgui 1.28.0
Activity and Diversity Analysis Module Graphical User Interface7 versions - Latest release: 5 months ago - 24.2 thousand downloads total - 1 maintainer
paxtoolsr 1.42.0 removed
Access Pathways from Multiple Databases Through BioPAX and Pathway Commons5 versions - Latest release: over 1 year ago - 27.7 thousand downloads total - 10 stars on GitHub - 1 maintainer
PanViz 1.10.0 removed
Integrating Multi-Omic Network Data With Summay-Level GWAS Data5 versions - Latest release: over 1 year ago - 3.39 thousand downloads total - 3 stars on GitHub - 1 maintainer
MIGSA 1.24.0 removed
Massive and Integrative Gene Set Analysis1 version - Latest release: about 3 years ago - 7.89 thousand downloads total - 0 stars on GitHub - 1 maintainer
ASpediaFI 1.14.0 removed
ASpedia-FI: Functional Interaction Analysis of Alternative Splicing Events1 version - Latest release: about 3 years ago - 3.82 thousand downloads total - 3 stars on GitHub - 1 maintainer
dce 1.13.0 removed
Pathway Enrichment Based on Differential Causal Effects4 versions - Latest release: almost 2 years ago - 6.79 thousand downloads total - 14 stars on GitHub - 1 maintainer
biodbKegg 1.11.0 removed
biodbKegg, a library for connecting to the KEGG Database5 versions - Latest release: almost 2 years ago - 4.81 thousand downloads total - 2 stars on GitHub - 1 maintainer
Top 9.3% on bioconductor.org
5 versions - Latest release: over 1 year ago - 1 dependent package - 42.4 thousand downloads total - 1 maintainer
MAGeCKFlute 2.12.0 removed
Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic Screens5 versions - Latest release: over 1 year ago - 1 dependent package - 42.4 thousand downloads total - 1 maintainer
PloGO2 1.16.0 removed
Plot Gene Ontology and KEGG pathway Annotation and Abundance3 versions - Latest release: over 2 years ago - 4.86 thousand downloads total - 2 maintainers
InterMineR 1.26.0 removed
R Interface with InterMine-Powered Databases4 versions - Latest release: over 2 years ago - 12 thousand downloads total - 17 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: almost 3 years ago - 7.94 thousand downloads total - 1 maintainer
netboxr 1.11.0 removed
netboxr1 version - Latest release: about 3 years ago - 2.92 thousand downloads total - 1 maintainer
Related Keywords
Software
68
Pathways
44
GeneSetEnrichment
28
GeneExpression
27
Network
23
GraphAndNetwork
23
GO
22
Reactome
18
Visualization
17
RNASeq
16
Clustering
12
ImmunoOncology
12
Metabolomics
11
DifferentialExpression
11
Sequencing
11
SystemsBiology
11
NetworkEnrichment
10
Annotation
10
Transcriptomics
9
Microarray
9
MultipleComparison
8
r
7
DataImport
7
GeneRegulation
7
Regression
7
SingleCell
7
Genetics
6
NetworkInference
6
Proteomics
5
ThirdPartyClient
5
Infrastructure
5
Normalization
5
BiomedicalInformatics
5
GeneTarget
5
Transcription
5
DataRepresentation
4
GenePrediction
4
Coverage
4
FunctionalPrediction
4
StatisticalMethod
4
Bayesian
4
GeneSignaling
3
Survival
3
bioinformatics
3
DNAMethylation
3
AlternativeSplicing
3
Classification
3
QualityControl
3
DimensionReduction
3
FeatureExtraction
2
Epigenetics
2
BioCarta
2
pathways
2
bioconductor
2
CellBiology
2
BatchEffect
2
TimeCourse
2
visualization
2
biology
2
Spatial
2
GenomeWideAssociation
2
SNP
2
FunctionalGenomics
2
kegg
2
WorkflowStep
2
GUI
2
Microbiome
2
metabolomics-pipeline
1
gene-sets
1
methylation
1
mskcc
1
longitudinal-analysis
1
metabolomics-data
1
TwoChannel
1
functional-analysis
1
gene-mutation
1
cancer
1
dynamics
1
gene-methylation
1
gene-expression
1
cancer-data
1
gene
1
MassSpectrometry
1
statistics
1
sqtl
1
splicing
1
rna-seq
1
ballgown
1
alternative-splicing
1
3s-scores
1
Preprocessing
1
DifferentialSplicing
1
ShinyApps
1
ReportWriting
1
r-package
1
cran
1
core-services
1
mRNAMicroarray
1
PrincipalComponent
1
package
1