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bioconductor.org "Pathways" keyword

gsean 1.32.0
Gene Set Enrichment Analysis with Networks
7 versions - Latest release: 4 months ago - 24.2 thousand downloads total - 1 maintainer
MetaboDynamics 2.2.1
Bayesian analysis of longitudinal metabolomics data
6 versions - Latest release: about 11 hours ago - 10.7 thousand downloads total - 5 stars on GitHub - 1 maintainer
Top 0.9% on bioconductor.org
annotate 1.90.0
Annotation for microarrays
8 versions - Latest release: 5 months ago - 48 dependent packages - 5.05 million downloads total - 1 maintainer
Top 0.6% on bioconductor.org
edgeR 4.10.5
Empirical Analysis of Digital Gene Expression Data in R
30 versions - Latest release: 3 days ago - 181 dependent packages - 4.73 million downloads total - 4 maintainers
pathwayPCA 1.28.0
Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection
7 versions - Latest release: 4 months ago - 1 dependent package - 24.7 thousand downloads total - 11 stars on GitHub - 1 maintainer
Top 2.1% on bioconductor.org
GOSemSim 2.38.3
GO-terms Semantic Similarity Measures
10 versions - Latest release: 2 months ago - 14 dependent packages - 2.38 million downloads total - 1 maintainer
carnation 1.0.1
Interactive Exploration & Management of RNA-Seq Analyses
2 versions - Latest release: 17 days ago - 4.68 thousand downloads total - 2 stars on GitHub - 1 maintainer
Top 1.9% on bioconductor.org
enrichplot 1.32.0
Visualization of Functional Enrichment Result
22 versions - Latest release: 5 months ago - 15 dependent packages - 2.69 million downloads total - 1 maintainer
GSReg 1.46.0
Gene Set Regulation (GS-Reg)
7 versions - Latest release: 4 months ago - 31.4 thousand downloads total - 2 maintainers
ssPATHS 1.26.0
ssPATHS: Single Sample PATHway Score
7 versions - Latest release: 4 months ago - 19 thousand downloads total - 1 maintainer
Top 4.2% on bioconductor.org
piano 2.28.0
Platform for integrative analysis of omics data
7 versions - Latest release: 4 months ago - 3 dependent packages - 123 thousand downloads total - 1 maintainer
iPath 1.18.0
iPath pipeline for detecting perturbed pathways at individual level
7 versions - Latest release: 4 months ago - 14.2 thousand downloads total - 2 stars on GitHub - 1 maintainer
Top 1.0% on bioconductor.org
fgsea 1.38.0
Fast Gene Set Enrichment Analysis
11 versions - Latest release: 5 months ago - 38 dependent packages - 2.63 million downloads total - 458 stars on GitHub - 1 maintainer
Top 9.8% on bioconductor.org
EGSEA 1.40.0
Ensemble of Gene Set Enrichment Analyses
8 versions - Latest release: 4 months ago - 1 dependent package - 52.9 thousand downloads total - 1 maintainer
Top 1.2% on bioconductor.org
clusterProfiler 4.20.0
A Universal Enrichment Tool for Interpreting Omics Data
20 versions - Latest release: 5 months ago - 59 dependent packages - 2.81 million downloads total - 1 maintainer
Top 1.6% on bioconductor.org
DOSE 4.6.0
Disease Ontology Semantic and Enrichment analysis
14 versions - Latest release: 5 months ago - 27 dependent packages - 2.61 million downloads total - 1 maintainer
Top 1.2% on bioconductor.org
KEGGREST 1.52.2
Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG)
6 versions - Latest release: 27 days ago - 35 dependent packages - 5.33 million downloads total - 1 maintainer
cpvSNP 1.44.0
Gene set analysis methods for SNP association p-values that lie in genes in given gene sets
7 versions - Latest release: 4 months ago - 31.6 thousand downloads total - 1 maintainer
ggkegg 1.10.0
Analyzing and visualizing KEGG information using the grammar of graphics
17 versions - Latest release: 4 months ago - 29.7 thousand downloads total - 247 stars on GitHub - 1 maintainer
Top 8.0% on bioconductor.org
pathRender 1.80.0
Render molecular pathways
7 versions - Latest release: 4 months ago - 47.6 thousand downloads total - 1 maintainer
PCAN 1.40.0
Phenotype Consensus ANalysis (PCAN)
7 versions - Latest release: 4 months ago - 27 thousand downloads total - 1 maintainer
coRdon 1.30.0
Codon Usage Analysis and Prediction of Gene Expressivity
7 versions - Latest release: 4 months ago - 34.2 thousand downloads total - 22 stars on GitHub - 1 maintainer
DART 1.60.0
Denoising Algorithm based on Relevance network Topology
7 versions - Latest release: 4 months ago - 41.4 thousand downloads total - 1 maintainer
MetaProViz 4.0.0
METabolomics pre-PRocessing, functiOnal analysis and VIZualisation
1 version - Latest release: 5 months ago - 4.84 thousand downloads total - 24 stars on GitHub - 1 maintainer
bioCancer 1.40.0
Interactive Multi-Omics Cancers Data Visualization and Analysis
9 versions - Latest release: 4 months ago - 30 thousand downloads total - 22 stars on GitHub - 1 maintainer
MetaboSignal 1.42.1
MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathways
9 versions - Latest release: about 1 month ago - 31.8 thousand downloads total - 2 maintainers
scGraphVerse 1.2.0
scGraphVerse: A Gene Network Analysis Package
2 versions - Latest release: 4 months ago - 5.78 thousand downloads total - 1 stars on GitHub - 1 maintainer
BioCartaImage 1.10.0
BioCarta Pathway Images
7 versions - Latest release: 4 months ago - 11.5 thousand downloads total - 11 stars on GitHub - 1 maintainer
gep2pep 1.32.0
Creation and Analysis of Pathway Expression Profiles (PEPs)
8 versions - Latest release: 9 days ago - 20.2 thousand downloads total - 1 maintainer
sparrow 1.18.0
Take command of set enrichment analyses through a unified interface
8 versions - Latest release: 4 months ago - 1 dependent package - 27.7 thousand downloads total - 23 stars on GitHub - 1 maintainer
Top 2.7% on bioconductor.org
TCGAbiolinks 2.40.0
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data
9 versions - Latest release: 4 months ago - 7 dependent packages - 644 thousand downloads total - 354 stars on GitHub - 2 maintainers
cosmosR 1.20.0
COSMOS (Causal Oriented Search of Multi-Omic Space)
8 versions - Latest release: 4 months ago - 18.5 thousand downloads total - 70 stars on GitHub - 1 maintainer
PathNet 1.52.0
An R package for pathway analysis using topological information
7 versions - Latest release: 4 months ago - 34.2 thousand downloads total - 1 maintainer
leapR 1.0.0
Layered enrichment analysis of pathways R
1 version - Latest release: 5 months ago - 3.66 thousand downloads total - 1 maintainer
Top 4.0% on bioconductor.org
GlobalAncova 4.30.0
Global test for groups of variables via model comparisons
7 versions - Latest release: 4 months ago - 165 thousand downloads total - 1 maintainer
Top 9.6% on bioconductor.org
NCIgraph 1.60.0
Pathways from the NCI Pathways Database
7 versions - Latest release: 5 months ago - 1 dependent package - 38.2 thousand downloads total - 1 maintainer
DeepTarget 1.6.0
Deep characterization of cancer drugs
4 versions - Latest release: 4 months ago - 9.16 thousand downloads total - 1 maintainer
Top 2.7% on bioconductor.org
globaltest 5.66.0
Testing Groups of Covariates/Features for Association with a Response Variable, with Applications...
7 versions - Latest release: 4 months ago - 6 dependent packages - 328 thousand downloads total - 1 maintainer
NetActivity 1.14.0
Compute gene set scores from a deep learning framework
7 versions - Latest release: 4 months ago - 12.4 thousand downloads total - 1 maintainer
pairkat 1.18.0
PaIRKAT
7 versions - Latest release: 4 months ago - 13.6 thousand downloads total - 0 stars on GitHub - 1 maintainer
MultiRNAflow 1.10.0
An R package for integrated analysis of temporal RNA-seq data with multiple biological conditions
6 versions - Latest release: 4 months ago - 12.2 thousand downloads total - 7 stars on GitHub - 1 maintainer
GOexpress 1.46.0
Visualise microarray and RNAseq data using gene ontology annotations
7 versions - Latest release: 4 months ago - 1 dependent package - 41.8 thousand downloads total - 10 stars on GitHub - 1 maintainer
MoonlightR 1.38.0
Identify oncogenes and tumor suppressor genes from omics data
7 versions - Latest release: 3 months ago - 26.3 thousand downloads total - 17 stars on GitHub - 1 maintainer
roastgsa 1.10.0
Rotation based gene set analysis
6 versions - Latest release: 4 months ago - 11.1 thousand downloads total - 0 stars on GitHub - 1 maintainer
CHRONOS 1.40.0
CHRONOS: A time-varying method for microRNA-mediated sub-pathway enrichment analysis
7 versions - Latest release: 4 months ago - 24.4 thousand downloads total - 1 maintainer
pathMED 1.4.0
Scoring Personalized Molecular Portraits
5 versions - Latest release: 3 months ago - 4.08 thousand downloads total - 5 stars on GitHub - 1 maintainer
CBNplot 1.12.0
plot bayesian network inferred from gene expression data based on enrichment analysis results
9 versions - Latest release: 4 months ago - 14.7 thousand downloads total - 68 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: 4 months ago - 50 thousand downloads total - 1 maintainer
Path2PPI 1.42.0
Prediction of pathway-related protein-protein interaction networks
7 versions - Latest release: 4 months ago - 26.4 thousand downloads total - 1 maintainer
GSEABenchmarkeR 1.32.0
Reproducible GSEA Benchmarking
8 versions - Latest release: 4 months ago - 2 dependent packages - 24.6 thousand downloads total - 14 stars on GitHub - 1 maintainer
paxtoolsr 1.42.0 removed
Access Pathways from Multiple Databases Through BioPAX and Pathway Commons
5 versions - Latest release: over 1 year ago - 27.7 thousand downloads total - 10 stars on GitHub - 1 maintainer
StarBioTrek 1.30.0 removed
StarBioTrek
3 versions - Latest release: over 2 years ago - 10.4 thousand downloads total - 0 stars on GitHub - 1 maintainer
EmpiricalBrownsMethod 1.40.0
Uses Brown's method to combine p-values from dependent tests
7 versions - Latest release: 3 months ago - 2 dependent packages - 28.3 thousand downloads total - 22 stars on GitHub - 1 maintainer
Top 2.7% on bioconductor.org
goseq 1.64.0
Gene Ontology analyser for RNA-seq and other length biased data
7 versions - Latest release: 4 months ago - 5 dependent packages - 325 thousand downloads total - 2 stars on GitHub - 1 maintainer
PFP 1.10.0 removed
Pathway Fingerprint Framework in R
2 versions - Latest release: almost 3 years ago - 1.82 thousand downloads total - 0 stars on GitHub - 1 maintainer
ASpediaFI 1.14.0 removed
ASpedia-FI: Functional Interaction Analysis of Alternative Splicing Events
1 version - Latest release: almost 3 years ago - 3.82 thousand downloads total - 3 stars on GitHub - 1 maintainer
rsemmed 1.22.0
An interface to the Semantic MEDLINE database
7 versions - Latest release: 3 months ago - 14.1 thousand downloads total - 0 stars on GitHub - 1 maintainer
islify 1.4.0
Automatic scoring and classification of cell-based assay images
3 versions - Latest release: 4 months ago - 6.51 thousand downloads total - 1 maintainer
anansi 1.2.0
Annotation-Based Analysis of Specific Interactions
2 versions - Latest release: 4 months ago - 5.28 thousand downloads total - 10 stars on GitHub - 1 maintainer
ASSIGN 1.48.0
Adaptive Signature Selection and InteGratioN (ASSIGN)
7 versions - Latest release: 5 months ago - 1 dependent package - 36.8 thousand downloads total - 2 stars on GitHub - 4 maintainers
TMSig 1.6.0
Tools for Molecular Signatures
4 versions - Latest release: 4 months ago - 8.18 thousand downloads total - 5 stars on GitHub - 1 maintainer
biodbKegg 1.11.0 removed
biodbKegg, a library for connecting to the KEGG Database
5 versions - Latest release: almost 2 years ago - 4.81 thousand downloads total - 2 stars on GitHub - 1 maintainer
Moonlight2R 1.10.1
Identify oncogenes and tumor suppressor genes from omics data
9 versions - Latest release: 2 months ago - 12.2 thousand downloads total - 5 stars on GitHub - 1 maintainer
scToppR 1.0.0
API Wrapper for ToppGene
1 version - Latest release: 5 months ago - 3.53 thousand downloads total - 8 stars on GitHub - 1 maintainer
fobitools 1.20.0
Tools for Manipulating the FOBI Ontology
7 versions - Latest release: 3 months ago - 14.7 thousand downloads total - 1 stars on GitHub - 1 maintainer
multiGSEA 1.22.0
Combining GSEA-based pathway enrichment with multi omics data integration
8 versions - Latest release: 5 months ago - 22.6 thousand downloads total - 23 stars on GitHub - 1 maintainer
LiquidAssociation 1.66.0
LiquidAssociation
7 versions - Latest release: 4 months ago - 1 dependent package - 40.7 thousand downloads total - 1 maintainer
mnem 1.28.0
Mixture Nested Effects Models
7 versions - Latest release: 3 months ago - 4 dependent packages - 22.7 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 7.5% on bioconductor.org
miRNApath 1.72.0
miRNApath: Pathway Enrichment for miRNA Expression Data
7 versions - Latest release: 4 months ago - 44.9 thousand downloads total - 1 maintainer
mitology 1.4.0
Study of mitochondrial activity from RNA-seq data
3 versions - Latest release: 4 months ago - 7.72 thousand downloads total - 2 stars on GitHub - 1 maintainer
CBN2Path 1.2.0
CBN2Path: an R/Bioconductor package for the analysis of cancer progression pathways using Conjunc...
3 versions - Latest release: 4 months ago - 4.43 thousand downloads total - 0 stars on GitHub - 2 maintainers
toppgene 1.0.2
Gene List Enrichment Analysis using the ToppGene Suite
3 versions - Latest release: about 1 month ago - 2.06 thousand downloads total - 1 stars on GitHub - 1 maintainer
iSEEpathways 1.10.0
iSEE extension for panels related to pathway analysis
6 versions - Latest release: 4 months ago - 11.2 thousand downloads total - 1 stars on GitHub - 1 maintainer
tidysbml 1.6.0
Extract SBML's data into dataframes
4 versions - Latest release: 4 months ago - 6.84 thousand downloads total - 2 stars on GitHub - 1 maintainer
DeeDeeExperiment 1.2.0
DeeDeeExperiment: An S4 Class for managing and exploring omics analysis results
2 versions - Latest release: 4 months ago - 6.04 thousand downloads total - 1 stars on GitHub - 1 maintainer
mirIntegrator 1.42.0
Integrating microRNA expression into signaling pathways for pathway analysis
7 versions - Latest release: 4 months ago - 26.6 thousand downloads total - 1 stars on GitHub - 1 maintainer
padma 1.22.0
Individualized Multi-Omic Pathway Deviation Scores Using Multiple Factor Analysis
9 versions - Latest release: 4 months ago - 15.8 thousand downloads total - 3 stars on GitHub - 1 maintainer
ReactomeContentService4R 1.16.0 removed
Interface for the Reactome Content Service
5 versions - Latest release: over 1 year ago - 1 dependent package - 7.41 thousand downloads total - 4 stars on GitHub - 1 maintainer
dmGsea 1.2.2
Efficient Gene Set Enrichment Analysis for DNA Methylation Data
6 versions - Latest release: 24 days ago - 6.69 thousand downloads total - 1 maintainer
esetVis 1.38.0
Visualizations of expressionSet Bioconductor object
8 versions - Latest release: 4 months ago - 27 thousand downloads total - 1 maintainer
funOmics 1.6.0
Aggregating Omics Data into Higher-Level Functional Representations
4 versions - Latest release: 3 months ago - 6.97 thousand downloads total - 7 stars on GitHub - 1 maintainer
gatom 1.10.2
Finding an Active Metabolic Module in Atom Transition Network
8 versions - Latest release: 2 months ago - 12.2 thousand downloads total - 8 stars on GitHub - 1 maintainer
Top 8.9% on bioconductor.org
CellNOptR 1.58.0
Training of boolean logic models of signalling networks using prior knowledge networks and pertur...
7 versions - Latest release: 4 months ago - 6 dependent packages - 57.3 thousand downloads total - 1 maintainer
Top 5.7% on bioconductor.org
rGREAT 2.14.0
GREAT Analysis - Functional Enrichment on Genomic Regions
8 versions - Latest release: 4 months ago - 3 dependent packages - 96.6 thousand downloads total - 99 stars on GitHub - 1 maintainer
ndexr 1.34.0
NDEx R client library
7 versions - Latest release: 4 months ago - 21.1 thousand downloads total - 9 stars on GitHub - 1 maintainer
SBGNview 1.26.0
"SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways"
7 versions - Latest release: 5 months ago - 23.2 thousand downloads total - 29 stars on GitHub - 1 maintainer
Top 10.0% on bioconductor.org
mgsa 1.60.0
Model-based gene set analysis
7 versions - Latest release: 4 months ago - 1 dependent package - 42.7 thousand downloads total - 5 stars on GitHub - 1 maintainer
Top 6.5% on bioconductor.org
goProfiles 1.74.0
goProfiles: an R package for the statistical analysis of functional profiles
7 versions - Latest release: 4 months ago - 1 dependent package - 60.5 thousand downloads total - 1 maintainer
pathlinkR 1.8.0
Analyze and interpret RNA-Seq results
6 versions - Latest release: 4 months ago - 11.2 thousand downloads total - 33 stars on GitHub - 1 maintainer
wppi 1.19.0
Weighting protein-protein interactions
8 versions - Latest release: 4 months ago - 13.7 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 2.7% on bioconductor.org
KEGGgraph 1.72.0
KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor
7 versions - Latest release: 4 months ago - 13 dependent packages - 824 thousand downloads total - 1 maintainer
PAST 1.28.0
Pathway Association Study Tool (PAST)
7 versions - Latest release: 4 months ago - 17.8 thousand downloads total - 5 stars on GitHub - 1 maintainer
pairedGSEA 1.12.0
Paired DGE and DGS analysis for gene set enrichment analysis
7 versions - Latest release: 4 months ago - 9.92 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 2.2% on bioconductor.org
GSVA 2.6.6
Gene Set Variation Analysis for Microarray and RNA-Seq Data
22 versions - Latest release: about 1 month ago - 15 dependent packages - 899 thousand downloads total - 247 stars on GitHub - 1 maintainer
methylGSA 1.30.0
Gene Set Analysis Using the Outcome of Differential Methylation
7 versions - Latest release: 4 months ago - 26.9 thousand downloads total - 13 stars on GitHub - 1 maintainer
epiNEM 1.36.0
epiNEM
7 versions - Latest release: 4 months ago - 4 dependent packages - 25.9 thousand downloads total - 1 stars on GitHub - 1 maintainer
cogena 1.46.0
co-expressed gene-set enrichment analysis
7 versions - Latest release: 4 months ago - 33.5 thousand downloads total - 12 stars on GitHub - 1 maintainer
Top 3.9% on bioconductor.org
pathview 1.52.0
a tool set for pathway based data integration and visualization
7 versions - Latest release: 4 months ago - 9 dependent packages - 741 thousand downloads total - 50 stars on GitHub - 1 maintainer
GeneTonic 3.6.0
Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional ...
7 versions - Latest release: 4 months ago - 1 dependent package - 28.8 thousand downloads total - 83 stars on GitHub - 1 maintainer
GeneAccord 1.18.0 removed
Detection of clonally exclusive gene or pathway pairs in a cohort of cancer patients
1 version - Latest release: almost 3 years ago - 4.41 thousand downloads total - 2 stars on GitHub - 1 maintainer
Related Keywords
Software 173 GeneSetEnrichment 83 GeneExpression 77 Network 62 GraphAndNetwork 48 KEGG 44 DifferentialExpression 43 GO 43 Visualization 40 RNASeq 37 SystemsBiology 33 Annotation 31 Microarray 30 NetworkEnrichment 25 Sequencing 24 Clustering 23 Reactome 23 ImmunoOncology 20 Transcriptomics 20 MultipleComparison 19 Genetics 17 Metabolomics 17 Transcription 16 Proteomics 15 NetworkInference 15 Classification 14 DataImport 13 GeneRegulation 13 BiomedicalInformatics 11 r 11 StatisticalMethod 11 FunctionalGenomics 11 Regression 11 GeneTarget 10 SingleCell 10 bioconductor 9 GeneSignaling 9 DNAMethylation 8 TimeCourse 8 Survival 8 CellBiology 8 bioinformatics 8 DataRepresentation 8 QualityControl 7 Normalization 7 Bayesian 7 DifferentialMethylation 7 PrincipalComponent 7 ReportWriting 7 GenePrediction 7 Preprocessing 6 OneChannel 6 Epigenetics 6 AlternativeSplicing 6 FeatureExtraction 5 DimensionReduction 5 FunctionalPrediction 5 BatchEffect 5 GUI 5 ShinyApps 5 ThirdPartyClient 5 GeneticVariability 4 MethylationArray 4 Coverage 4 shiny 4 GenomicVariation 4 CRISPR 4 Infrastructure 4 bioconductor-package 4 miRNA 4 mRNAMicroarray 4 pathways 4 BioCarta 4 enrichment-analysis 3 visualization 3 transcriptomics 3 PooledScreens 3 ATACSeq 3 r-package 3 DifferentialSplicing 3 GenomeWideAssociation 3 pathway-analysis 3 SNP 3 TwoChannel 3 networks 2 GenomeAnnotation 2 MethylSeq 2 CopyNumberVariation 2 computational-biology 2 bayesian 2 Cheminformatics 2 DNASeq 2 gene-expression 2 network 2 CellBasedAssays 2 gene-sets 2 ontology 2 MassSpectrometry 2 ChIPSeq 2 cancer 2