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bioconductor.org "Pathways" keyword

View the packages on the bioconductor.org package registry that are tagged with the "Pathways" keyword.

mirIntegrator 1.38.0
Integrating microRNA expression into signaling pathways for pathway analysis
5 versions - Latest release: 3 months ago - 16.8 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 0.9% on bioconductor.org
annotate 1.86.1
Annotation for microarrays
6 versions - Latest release: about 1 month ago - 48 dependent packages - 4.05 million downloads total - 1 maintainer
sparrow 1.14.0
Take command of set enrichment analyses through a unified interface
6 versions - Latest release: 3 months ago - 1 dependent package - 13.5 thousand downloads total - 21 stars on GitHub - 1 maintainer
MOSClip 1.2.2
Multi Omics Survival Clip
4 versions - Latest release: about 1 month ago - 1.85 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 1.2% on bioconductor.org
clusterProfiler 4.16.0
A universal enrichment tool for interpreting omics data
14 versions - Latest release: 3 months ago - 59 dependent packages - 1.93 million downloads total - 1 maintainer
Top 2.7% on bioconductor.org
KEGGgraph 1.68.0
KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor
5 versions - Latest release: 2 months ago - 13 dependent packages - 644 thousand downloads total - 1 maintainer
Top 1.0% on bioconductor.org
fgsea 1.34.2
Fast Gene Set Enrichment Analysis
8 versions - Latest release: 12 days ago - 38 dependent packages - 1.73 million downloads total - 345 stars on GitHub - 1 maintainer
Top 1.6% on bioconductor.org
DOSE 4.2.0
Disease Ontology Semantic and Enrichment analysis
12 versions - Latest release: 3 months ago - 27 dependent packages - 1.75 million downloads total - 1 maintainer
BioCor 1.32.0
Functional similarities
5 versions - Latest release: 2 months ago - 18.6 thousand downloads total - 14 stars on GitHub - 1 maintainer
Top 0.6% on bioconductor.org
edgeR 4.6.3
Empirical Analysis of Digital Gene Expression Data in R
23 versions - Latest release: 16 days ago - 181 dependent packages - 3.6 million downloads total - 4 maintainers
rrvgo 1.20.0
Reduce + Visualize GO
7 versions - Latest release: 3 months ago - 30.3 thousand downloads total - 30 stars on GitHub - 1 maintainer
Top 1.9% on bioconductor.org
enrichplot 1.28.4
Visualization of Functional Enrichment Result
15 versions - Latest release: 9 days ago - 15 dependent packages - 1.73 million downloads total - 1 maintainer
NetPathMiner 1.44.0
NetPathMiner for Biological Network Construction, Path Mining and Visualization
5 versions - Latest release: 3 months ago - 23.7 thousand downloads total - 9 stars on GitHub - 1 maintainer
fedup 1.16.0
Fisher's Test for Enrichment and Depletion of User-Defined Pathways
5 versions - Latest release: 3 months ago - 6.8 thousand downloads total - 7 stars on GitHub - 1 maintainer
MetaboDynamics 1.0.2
Bayesian analysis of longitudinal metabolomics data
2 versions - Latest release: about 1 month ago - 1.59 thousand downloads total - 5 stars on GitHub - 1 maintainer
Top 2.3% on bioconductor.org
GOstats 2.74.0
Tools for manipulating GO and microarrays
5 versions - Latest release: 3 months ago - 23 dependent packages - 534 thousand downloads total - 1 maintainer
mnem 1.24.0
Mixture Nested Effects Models
5 versions - Latest release: 3 months ago - 4 dependent packages - 13.1 thousand downloads total - 4 stars on GitHub - 1 maintainer
GeDi 1.4.0
Defining and visualizing the distances between different genesets
4 versions - Latest release: 3 months ago - 3.29 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 6.4% on bioconductor.org
annaffy 1.80.0
Annotation tools for Affymetrix biological metadata
5 versions - Latest release: 2 months ago - 2 dependent packages - 386 thousand downloads total - 1 maintainer
Top 6.1% on bioconductor.org
EnrichmentBrowser 2.38.0
Seamless navigation through combined results of set-based and network-based enrichment analysis
5 versions - Latest release: 2 months ago - 5 dependent packages - 62.5 thousand downloads total - 19 stars on GitHub - 1 maintainer
hipathia 3.8.0
HiPathia: High-throughput Pathway Analysis
5 versions - Latest release: 3 months ago - 16.8 thousand downloads total - 1 maintainer
GOexpress 1.42.0
Visualise microarray and RNAseq data using gene ontology annotations
5 versions - Latest release: 2 months ago - 1 dependent package - 29.4 thousand downloads total - 9 stars on GitHub - 1 maintainer
Top 2.7% on bioconductor.org
TCGAbiolinks 2.36.0
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data
7 versions - Latest release: 2 months ago - 7 dependent packages - 474 thousand downloads total - 321 stars on GitHub - 2 maintainers
islify 1.0.0
Automatic scoring and classification of cell-based assay images
1 version - Latest release: 3 months ago - 920 downloads total - 1 maintainer
FELLA 1.28.0
Interpretation and enrichment for metabolomics data
5 versions - Latest release: 3 months ago - 19.5 thousand downloads total - 1 maintainer
cTRAP 1.26.0
Identification of candidate causal perturbations from differential gene expression data
6 versions - Latest release: 3 months ago - 11.5 thousand downloads total - 5 stars on GitHub - 1 maintainer
rsemmed 1.18.0
An interface to the Semantic MEDLINE database
5 versions - Latest release: 2 months ago - 7.23 thousand downloads total - 0 stars on GitHub - 1 maintainer
GSReg 1.42.0
Gene Set Regulation (GS-Reg)
5 versions - Latest release: 2 months ago - 19 thousand downloads total - 2 maintainers
pathMED 1.0.2
Scoring Personalized Molecular Portraits
3 versions - Latest release: 29 days ago - 863 downloads total - 5 stars on GitHub - 1 maintainer
multiGSEA 1.18.0
Combining GSEA-based pathway enrichment with multi omics data integration
6 versions - Latest release: 3 months ago - 12.7 thousand downloads total - 19 stars on GitHub - 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
gatom 1.6.0
Finding an Active Metabolic Module in Atom Transition Network
4 versions - Latest release: 3 months ago - 4.57 thousand downloads total - 7 stars on GitHub - 1 maintainer
ChromSCape 1.17.0
Analysis of single-cell epigenomics datasets with a Shiny App
5 versions - Latest release: 2 months ago - 7.92 thousand downloads total - 14 stars on GitHub - 1 maintainer
MultiRNAflow 1.6.0
An R package for integrated analysis of temporal RNA-seq data with multiple biological conditions
4 versions - Latest release: 3 months ago - 4.66 thousand downloads total - 0 stars on GitHub - 1 maintainer
GenomicSuperSignature 1.16.1
Interpretation of RNA-seq experiments through robust, efficient comparison to public databases
6 versions - Latest release: 2 months ago - 7.45 thousand downloads total - 12 stars on GitHub - 1 maintainer
funOmics 1.2.0
Aggregating Omics Data into Higher-Level Functional Representations
2 versions - Latest release: 3 months ago - 2.34 thousand downloads total - 6 stars on GitHub - 1 maintainer
GSEABenchmarkeR 1.28.1
Reproducible GSEA Benchmarking
6 versions - Latest release: about 2 months ago - 2 dependent packages - 14.3 thousand downloads total - 13 stars on GitHub - 1 maintainer
GWENA 1.18.0
Pipeline for augmented co-expression analysis
5 versions - Latest release: 3 months ago - 13.6 thousand downloads total - 18 stars on GitHub - 1 maintainer
iPath 1.14.0
iPath pipeline for detecting perturbed pathways at individual level
5 versions - Latest release: 3 months ago - 5.55 thousand downloads total - 2 stars on GitHub - 1 maintainer
OmnipathR 3.16.0
OmniPath web service client and more
7 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 information
5 versions - Latest release: 3 months ago - 24.9 thousand downloads total - 1 maintainer
DeepTarget 1.2.0
Deep characterization of cancer drugs
2 versions - Latest release: 3 months ago - 2.29 thousand downloads total - 1 maintainer
hypeR 2.5.0
An R Package For Geneset Enrichment Workflows
5 versions - Latest release: 3 months ago - 13.3 thousand downloads total - 76 stars on GitHub - 1 maintainer
Top 2.8% on bioconductor.org
ReactomePA 1.52.0
Reactome Pathway Analysis
5 versions - Latest release: 3 months ago - 15 dependent packages - 506 thousand downloads total - 1 maintainer
RCX 1.12.0
R package implementing the Cytoscape Exchange (CX) format
5 versions - Latest release: 3 months ago - 1 dependent package - 7.22 thousand downloads total - 8 stars on GitHub - 1 maintainer
coRdon 1.26.0
Codon Usage Analysis and Prediction of Gene Expressivity
5 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 Interface
5 versions - Latest release: 3 months ago - 12.4 thousand downloads total - 1 maintainer
ReactomeGraph4R 1.16.0
Interface for the Reactome Graph Database
6 versions - Latest release: 3 months ago - 4.21 thousand downloads total - 6 stars on GitHub - 1 maintainer
Top 2.7% on bioconductor.org
goseq 1.60.0
Gene Ontology analyser for RNA-seq and other length biased data
5 versions - Latest release: 3 months ago - 5 dependent packages - 251 thousand downloads total - 2 stars on GitHub - 1 maintainer
MIRit 1.4.1
Integrate microRNA and gene expression to decipher pathway complexity
5 versions - Latest release: about 2 months ago - 3.69 thousand downloads total - 1 stars on GitHub - 1 maintainer
TMSig 1.2.0
Tools for Molecular Signatures
2 versions - Latest release: 3 months ago - 1.72 thousand downloads total - 4 stars on GitHub - 1 maintainer
ndexr 1.30.0
NDEx R client library
5 versions - Latest release: 2 months ago - 14 thousand downloads total - 9 stars on GitHub - 1 maintainer
cosmosR 1.16.0
COSMOS (Causal Oriented Search of Multi-Omic Space)
5 versions - Latest release: 3 months ago - 8.53 thousand downloads total - 61 stars on GitHub - 1 maintainer
gsean 1.28.0
Gene Set Enrichment Analysis with Networks
5 versions - Latest release: 3 months ago - 12.3 thousand downloads total - 1 maintainer
Top 2.7% on bioconductor.org
graphite 1.54.0
GRAPH Interaction from pathway Topological Environment
5 versions - Latest release: 3 months ago - 11 dependent packages - 295 thousand downloads total - 8 stars on GitHub - 1 maintainer
bnem 1.16.0
Training of logical models from indirect measurements of perturbation experiments
5 versions - Latest release: 3 months ago - 7.04 thousand downloads total - 2 stars on GitHub - 1 maintainer
LiquidAssociation 1.62.0
LiquidAssociation
5 versions - Latest release: 3 months ago - 1 dependent package - 31.8 thousand downloads total - 1 maintainer
Top 7.8% on bioconductor.org
keggorthology 2.60.0
graph support for KO, KEGG Orthology
5 versions - Latest release: 3 months ago - 1 dependent package - 45.3 thousand downloads total - 1 maintainer
Top 9.8% on bioconductor.org
occugene 1.68.0
Functions for Multinomial Occupancy Distribution
5 versions - Latest release: 3 months ago - 30 thousand downloads total - 1 maintainer
SurfR 1.4.1
Surface Protein Prediction and Identification
8 versions - Latest release: 24 days ago - 3.48 thousand downloads total - 0 stars on GitHub - 1 maintainer
oppar 1.36.1
Outlier profile and pathway analysis in R
6 versions - Latest release: about 2 months ago - 14.3 thousand downloads total - 1 maintainer
ggkegg 1.6.0
Analyzing and visualizing KEGG information using the grammar of graphics
14 versions - Latest release: 3 months ago - 14.4 thousand downloads total - 229 stars on GitHub - 1 maintainer
Top 9.6% on bioconductor.org
NCIgraph 1.56.0
Pathways from the NCI Pathways Database
5 versions - Latest release: 3 months ago - 1 dependent package - 31 thousand downloads total - 1 maintainer
fastLiquidAssociation 1.44.0
functions for genome-wide application of Liquid Association
5 versions - Latest release: 3 months ago - 19.9 thousand downloads total - 1 maintainer
PhenoGeneRanker 1.16.0
PhenoGeneRanker: A gene and phenotype prioritization tool
5 versions - Latest release: 3 months ago - 5.74 thousand downloads total - 1 maintainer
Top 4.9% on bioconductor.org
rsbml 2.66.0
R support for SBML, using libsbml
5 versions - Latest release: 3 months ago - 3 dependent packages - 59.8 thousand downloads total - 1 maintainer
mitology 1.0.0
Study of mitochondrial activity from RNA-seq data
1 version - Latest release: 3 months ago - 1.07 thousand downloads total - 2 stars on GitHub - 1 maintainer
PanomiR 1.12.0
Detection of miRNAs that regulate interacting groups of pathways
5 versions - Latest release: 3 months ago - 5.61 thousand downloads total - 3 stars on GitHub - 1 maintainer
PAST 1.24.0
Pathway Association Study Tool (PAST)
5 versions - Latest release: 3 months ago - 9.28 thousand downloads total - 5 stars on GitHub - 1 maintainer
iSEEpathways 1.6.0
iSEE extension for panels related to pathway analysis
4 versions - Latest release: 3 months ago - 4.02 thousand downloads total - 1 stars on GitHub - 1 maintainer
tidysbml 1.2.0
Extract SBML's data into dataframes
2 versions - Latest release: 3 months ago - 1.76 thousand downloads total - 1 stars on GitHub - 1 maintainer
Path2PPI 1.38.0
Prediction of pathway-related protein-protein interaction networks
5 versions - Latest release: 3 months ago - 17.2 thousand downloads total - 1 maintainer
ASSIGN 1.44.0
Adaptive Signature Selection and InteGratioN (ASSIGN)
5 versions - Latest release: 3 months ago - 1 dependent package - 24.7 thousand downloads total - 2 stars on GitHub - 4 maintainers
nempi 1.16.0
Inferring unobserved perturbations from gene expression data
5 versions - Latest release: 3 months ago - 6.41 thousand downloads total - 2 stars on GitHub - 1 maintainer
gep2pep 1.28.0
Creation and Analysis of Pathway Expression Profiles (PEPs)
5 versions - Latest release: 3 months ago - 11.5 thousand downloads total - 1 maintainer
Top 4.6% on bioconductor.org
qpgraph 2.42.0
Estimation of Genetic and Molecular Regulatory Networks from High-Throughput Genomics Data
5 versions - Latest release: 3 months ago - 1 dependent package - 61.3 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 10.0% on bioconductor.org
mgsa 1.56.0
Model-based gene set analysis
5 versions - Latest release: 3 months ago - 1 dependent package - 33.4 thousand downloads total - 5 stars on GitHub - 1 maintainer
cpvSNP 1.40.0
Gene set analysis methods for SNP association p-values that lie in genes in given gene sets
5 versions - Latest release: 3 months ago - 17.8 thousand downloads total - 1 maintainer
Top 7.5% on bioconductor.org
miRNApath 1.68.0
miRNApath: Pathway Enrichment for miRNA Expression Data
5 versions - Latest release: 3 months ago - 36.9 thousand downloads total - 1 maintainer
PCAN 1.36.0
Phenotype Consensus ANalysis (PCAN)
5 versions - Latest release: 3 months ago - 15.1 thousand downloads total - 1 maintainer
easier 1.14.0
Estimate Systems Immune Response from RNA-seq data
5 versions - Latest release: 3 months ago - 8.44 thousand downloads total - 1 maintainer
Top 2.2% on bioconductor.org
GSVA 2.2.0
Gene Set Variation Analysis for Microarray and RNA-Seq Data
14 versions - Latest release: 3 months ago - 15 dependent packages - 554 thousand downloads total - 217 stars on GitHub - 1 maintainer
fobitools 1.16.0
Tools for Manipulating the FOBI Ontology
5 versions - Latest release: 3 months ago - 6.81 thousand downloads total - 1 stars on GitHub - 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
KnowSeq 1.22.0
KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline
5 versions - Latest release: 3 months ago - 10.2 thousand downloads total - 1 maintainer
CTDquerier 2.16.0
Package for CTDbase data query, visualization and downstream analysis
5 versions - Latest release: 3 months ago - 9.52 thousand downloads total - 1 maintainer
DART 1.56.0
Denoising Algorithm based on Relevance network Topology
5 versions - Latest release: 3 months ago - 29.2 thousand downloads total - 1 maintainer
wppi 1.16.0
Weighting protein-protein interactions
5 versions - Latest release: 3 months ago - 7.38 thousand downloads total - 1 stars on GitHub - 1 maintainer
pairedGSEA 1.8.0
Paired DGE and DGS analysis for gene set enrichment analysis
5 versions - Latest release: 3 months ago - 3.85 thousand downloads total - 2 stars on GitHub - 1 maintainer
ssPATHS 1.22.0
ssPATHS: Single Sample PATHway Score
5 versions - Latest release: 3 months ago - 8.11 thousand downloads total - 1 maintainer
methylGSA 1.26.0
Gene Set Analysis Using the Outcome of Differential Methylation
5 versions - Latest release: 3 months ago - 16.5 thousand downloads total - 12 stars on GitHub - 1 maintainer
Top 2.6% on bioconductor.org
Category 2.74.0
Category Analysis
5 versions - Latest release: 3 months ago - 13 dependent packages - 545 thousand downloads total - 1 maintainer
transomics2cytoscape 1.18.0
A tool set for 3D Trans-Omic network visualization with Cytoscape
6 versions - Latest release: 3 months ago - 7.69 thousand downloads total - 1 maintainer
pairkat 1.14.0
PaIRKAT
5 versions - Latest release: 3 months ago - 6 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 9.8% on bioconductor.org
FGNet 3.42.0
Functional Gene Networks derived from biological enrichment analyses
5 versions - Latest release: 3 months ago - 1 dependent package - 31.8 thousand downloads total - 1 maintainer
PPInfer 1.34.0
Inferring functionally related proteins using protein interaction networks
5 versions - Latest release: 3 months ago - 1 dependent package - 17.2 thousand downloads total - 1 maintainer
bioCancer 1.36.0
Interactive Multi-Omics Cancers Data Visualization and Analysis
7 versions - Latest release: 3 months ago - 16.9 thousand downloads total - 21 stars on GitHub - 1 maintainer
NetActivity 1.10.0
Compute gene set scores from a deep learning framework
5 versions - Latest release: 3 months ago - 4.86 thousand downloads total - 1 maintainer
Top 8.0% on bioconductor.org
pathRender 1.76.0
Render molecular pathways
5 versions - Latest release: 3 months ago - 35 thousand downloads total - 1 maintainer
Top 9.8% on bioconductor.org
EGSEA 1.36.0
Ensemble of Gene Set Enrichment Analyses
6 versions - Latest release: 3 months ago - 1 dependent package - 34.5 thousand downloads total - 1 maintainer
Related Keywords
Software 162 GeneSetEnrichment 77 GeneExpression 71 Network 60 GraphAndNetwork 46 KEGG 42 DifferentialExpression 41 GO 40 Visualization 36 RNASeq 36 SystemsBiology 31 Annotation 30 Microarray 29 NetworkEnrichment 23 Reactome 22 Sequencing 21 ImmunoOncology 20 Clustering 20 MultipleComparison 19 Transcriptomics 16 Genetics 16 Metabolomics 15 Classification 14 NetworkInference 14 Transcription 14 DataImport 13 GeneRegulation 12 Proteomics 12 r 11 FunctionalGenomics 11 BiomedicalInformatics 11 Regression 10 StatisticalMethod 10 GeneTarget 10 bioconductor 9 GeneSignaling 9 bioinformatics 8 Survival 8 CellBiology 8 TimeCourse 8 SingleCell 8 GenePrediction 7 DNAMethylation 7 DifferentialMethylation 7 ReportWriting 7 Normalization 7 PrincipalComponent 7 DataRepresentation 7 Bayesian 6 AlternativeSplicing 6 Preprocessing 6 QualityControl 6 OneChannel 6 Epigenetics 6 FunctionalPrediction 5 DimensionReduction 5 FeatureExtraction 5 BatchEffect 5 MethylationArray 4 miRNA 4 GeneticVariability 4 bioconductor-package 4 BioCarta 4 shiny 4 mRNAMicroarray 4 ShinyApps 4 ThirdPartyClient 4 GUI 4 pathways 4 CRISPR 4 Infrastructure 3 pathway-analysis 3 GenomeWideAssociation 3 SNP 3 enrichment-analysis 3 GenomicVariation 3 transcriptomics 3 DifferentialSplicing 3 Coverage 3 visualization 3 TwoChannel 3 ATACSeq 3 PooledScreens 3 r-package 3 MethylSeq 2 gene-sets 2 gene 2 kegg 2 SomaticMutation 2 MathematicalBiology 2 cancer 2 GenomeAnnotation 2 ChIPSeq 2 computational-biology 2 networks 2 MassSpectrometry 2 gene-ontology 2 gene-expression 2 ontology 2 Cheminformatics 2