Biocview "Pathways"

Activity and Diversity Analysis Module Graphical User Interface
Activity and Diversity Analysis Module Graphical User Interface
ADAM: Activity and Diversity Analysis Module
ADAM: Activity and Diversity Analysis Module
Adaptive Signature Selection and InteGratioN (ASSIGN)
Adaptive Signature Selection and InteGratioN (ASSIGN)
Adaptive Signature Selection and InteGratioN (ASSIGN)
A gene-signature ranking method based on sample density in PCA space
A metagenomic pipeline for systems biology
Analysis for short time-series data
Analysis for short time-series data
Analysis for short time-series data
Analysis of single-cell epigenomics datasets with a Shiny App
Analysis of single-cell epigenomics datasets with a Shiny App
An annotation and visualization package for multi-types and multi-groups expression data in KEGG pathway
An annotation and visualization package for multi-types and multi-groups expression data in KEGG pathway
An integrated analysis package of miRNA and mRNA expression data
An integrated analysis package of miRNA and mRNA expression data
An interface to the Semantic MEDLINE database
An interface to the Semantic MEDLINE database
Annotation for microarrays
Annotation for microarrays
Annotation tools for Affymetrix biological metadata
An R Package For Geneset Enrichment Workflows
An R Package For Geneset Enrichment Workflows
An R package for pathway analysis using topological information
An R package for pathway analysis using topological information
An R Package for Unbiased Splicing Pathway Analysis
An R Package for Unbiased Splicing Pathway Analysis in RNAseq data
ASpedia-FI: Functional Interaction Analysis of Alternative Splicing Events
ASpedia-FI: Functional Interaction Analysis of Alternative Splicing Events
A Systems Biology Approach for Drug Repurposing
Atlas and Analysis of Systems-Biology-Led Pathways
A tool set for 3D Trans-Omic network visualization with Cytoscape
A tool set for 3D Trans-Omic network visualization with Cytoscape
a tool set for pathway based data integration and visualization
a tool set for pathway based data integration and visualization
a tool set for pathway based data integration and visualization
a tool set for pathway based data integration and visualization
a tool set for pathway based data integration and visualization
A unified interface to a plethora of gene set enrichment analysis methods
Better prediction by use of co-data: Adaptive group-regularized ridge regression
Better prediction by use of co-data: Adaptive group-regularized ridge regression
BIMEGA: BIvariate Methylation and Expression GAussian mixture model
Bioc2019PanCancerStudy
biodbKegg, a library for connecting to the KEGG Database
Biological Network Analysis
Biological Network Analysis
BioMM: Biological-informed Multi-stage Machine learning framework for phenotype prediction using omics data
BioMM: Biological-informed Multi-stage Machine learning framework for phenotype prediction using omics data
BioMM: Biological-informed Multi-stage Machine learning framework for phenotype prediction using omics data
BLMA: A package for bi-level meta-analysis
BLMA: A package for bi-level meta-analysis
Build Annotation From Online Database
Category Analysis
Category Analysis
CHRONOS: A time-varying method for microRNA-mediated sub-pathway enrichment analysis
Client for GREAT Analysis
Client for GREAT Analysis
Client for GREAT Analysis
Client-side REST access KEGG
Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG)
Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG)
CNCDriver
Codon Usage Analysis and Prediction of Gene Expressivity
Codon Usage Analysis and Prediction of Gene Expressivity
co-expressed gene-set enrichment analysis
co-expressed gene-set enrichment analysis
Co-expression Modules identification Tool
Co-expression Modules identification Tool
Combining GSEA-based pathway enrichment with multi omics data integration
Combining GSEA-based pathway enrichment with multi omics data integration
CompositeDriver
Computation of functional similarities between GO terms and gene products; GO enrichment analysis
COSMOS (Causal Oriented Search of Multi-Omic Space)
Creation and Analysis of Pathway Expression Profiles (PEPs)
Creation and Analysis of Pathway Expression Profiles (PEPs)
CTDPathSim: Cell line-tumor deconvoluted pathway-based similarity in the context of precision medicine in cancer
Data package for query/retrieval of species specific MSigDB versions
Data package for query/retrieval of species specific MSigDB versions
Denoising Algorithm based on Relevance network Topology
DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq expression experiments
DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq expression experiments
Detection of clonally exclusive gene or pathway pairs in a cohort of cancer patients
dgeAnalysis
dgeAnalysis
Disease Ontology Semantic and Enrichment analysis
Disease Ontology Semantic and Enrichment analysis
Disease Ontology Semantic and Enrichment analysis
Disease Ontology Semantic and Enrichment analysis
dycone - analyze the dynamic landscape of metabolome data
(Dynamic) Nested Effects Models and Deterministic Effects Propagation Networks to reconstruct phenotypic hierarchies
Easy single cell analysis platform for enrichment
Easy single cell analysis platform for enrichment
Efficient, Scalable, and Reproducible Enrichment Workflows
Empirical Analysis of Digital Gene Expression Data in R
Empirical Analysis of Digital Gene Expression Data in R
Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional Enrichment Analysis
Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional Enrichment Analysis
Ensemble of Gene Set Enrichment Analyses
Ensemble of Gene Set Enrichment Analyses
epiNEM
epiNEM
ESEA: Discovering the Dysregulated Pathways based on Edge Set Enrichment Analysis
ESEA: Discovering the Dysregulated Pathways based on Edge Set Enrichment Analysis
Estimation of genetic and molecular regulatory networks from high-throughput genomics data
Estimation of genetic and molecular regulatory networks from high-throughput genomics data
Exploration and Significant Biology on a Gene Set.
Fast Gene Set Enrichment Analysis
Fast Gene Set Enrichment Analysis
FCBF-based Co-Expression Networks for Single Cells
FCBF-based Co-Expression Networks for Single Cells
FCBF-based Co-Expression Networks for Single Cells
Finding an Active Metabolic Module in Atom Transition Network
Fisher's Test for Enrichment and Depletion of User-Defined Pathways
Fisher's Test for Enrichment and Depletion of User-Defined Pathways
Functional analysis of metabolic and transcriptomic data
Functional analysis of metabolic and transcriptomic data
Functional Enrichment analysis
Functional Enrichment analysis
Functional Gene Networks derived from biological enrichment analyses
Functional similarities
Functional similarities
functions for genome-wide application of Liquid Association
functions for genome-wide application of Liquid Association
Functions for Multinomial Occupancy Distribution
Generally Applicable Gene-set Enrichment for Pathway Analysis
Gene set analysis methods for SNP association p-values that lie in genes in given gene sets
Gene Set Analysis Using the Outcome of Differential Methylation
Gene Set Analysis Using the Outcome of Differential Methylation
Gene Set Analysis Using the Outcome of Differential Methylation
Gene Set Enrichment Analysis with Networks
Gene Set Enrichment Analysis with Networks
Geneset enrichment based on InterPro domain signatures
Gene-set Enrichment with Regularized Regression
Gene-set Enrichment with Regularized Regression
Gene Set Regulation (GS-Reg)
Gene Set Regulation (GS-Reg)
Gene Set Regulation (GS-Reg)
Gene Set Variation Analysis for microarray and RNA-seq data
Gene Set Variation Analysis for microarray and RNA-seq data
Genomic Knowledge-guided Multiple Testing
Global test for groups of variables via model comparisons
Global test for groups of variables via model comparisons
GO-function: deriving biologcially relevant functions from statistically significant functions
goProfiles: an R package for the statistical analysis of functional profiles
goProfiles: an R package for the statistical analysis of functional profiles
GO-terms Semantic Similarity Measures
GO-terms Semantic Similarity Measures
GO-terms Semantic Similarity Measures
GRAPH Interaction from pathway Topological Environment
GRAPH Interaction from pathway Topological Environment
graph support for KO, KEGG Orthology
HiPathia: High-throughput Pathway Analysis
HiPathia: High-throughput Pathway Analysis
HiPathia: High-throughput Pathway Analysis
Identification of candidate causal perturbations from differential gene expression data
Identification of candidate causal perturbations from differential gene expression data
Identify oncogenes and tumor suppressor genes from omics data
Identify oncogenes and tumor suppressor genes from omics data
Individualized Multi-Omic Pathway Deviation Scores Using Multiple Factor Analysis
Individualized Multi-Omic Pathway Deviation Scores Using Multiple Factor Analysis
Inferring functionally related proteins using protein interaction networks
Inferring functionally related proteins using protein interaction networks
Inferring unobserved perturbations from gene expression data
Integrating microRNA expression into signaling pathways for pathway analysis
Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic Screens
Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic Screens
Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection
Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection
Interactive Multi-Omics Cancers Data Visualization and Analysis
Interactive Multi-Omics Cancers Data Visualization and Analysis
Interface for the Reactome Content Service
Interface for the Reactome Graph Database
Interpretation and enrichment for metabolomics data
Interpretation and enrichment for metabolomics data
Interpretation of RNA-seq experiments through robust, efficient comparison to public databases
Interpretation of RNA-seq experiments through robust, efficient comparison to public databases
JODA algorithm for quantifying gene deregulation using knowledge
KEGG analysis and visualizing of differentially expressed genes
KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor
KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor
KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline
KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline
Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene and Pathway Level
Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene and Pathway Level
LiquidAssociation
Meta-analysis of high-throughput experiments using feature annotations
Meta-analysis of high-throughput experiments using feature annotations
Meta-analysis of high-throughput experiments using feature annotations
Metabolite Set Enrichment Analysis (MSEA)
MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathways
Methods to Find Pathways with Significantly Different Variability
Methods to Find Pathways with Significantly Different Variability
Methods to Find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor Landscape
Methods to Find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor Landscape
MethylMix: Identifying methylation driven cancer genes
MethylMix: Identifying methylation driven cancer genes
MethylMix: Identifying methylation driven cancer genes
'MicroRNA' Set Enrichment Analysis
'MicroRNA' Set Enrichment Analysis
miRNApath: Pathway Enrichment for miRNA Expression Data
Mixture Nested Effects Models
Mixture Nested Effects Models
Model-based gene set analysis
Model-based gene set analysis
Multi Dimensional Gene Set Analysis.
Multi Dimensional Gene Set Analysis.
Multi-omics Classification, Functional Enrichment and Network Inference analysis
Multivariate and directional gene set testing
Multivariate and directional gene set testing
Murine Palate miRNA Expression Analysis
NDEx R client library
NDEx R client library
netboxr
netboxr
NetPathMiner for Biological Network Construction, Path Mining and Visualization
NetPathMiner for Biological Network Construction, Path Mining and Visualization
NetPathMiner for Biological Network Construction, Path Mining and Visualization
OmniPath web service client
OmniPath web service client and more
Outlier profile and pathway analysis in R
Outlier profile and pathway analysis in R
Overlay omics data onto SBGN pathway diagram
Package for CTDbase data query, visualization and downstream analysis
Package for CTDbase data query, visualization and downstream analysis
Pathway Association Study Tool (PAST)
Pathway Association Study Tool (PAST)
Pathway Enrichment Analysis Based on Bayesian Network
Pathway Enrichment Analysis Based on Bayesian Network
Pathway Fingerprint Framework in R
Pathways from the NCI Pathways Database
PaxtoolsR: Access Pathways from Multiple Databases through BioPAX and Pathway Commons
PaxtoolsR: Access Pathways from Multiple Databases through BioPAX and Pathway Commons
PaxtoolsR: Access Pathways from Multiple Databases through BioPAX and Pathway Commons
PEBBA
Permutation approximation methods for gene set enrichment analysis (non-permutation GSEA)
PhenoGeneRanker: A gene and phenotype prioritization tool
Phenotype Consensus ANalysis (PCAN)
Pipeline for augmented co-expression analysis
Pipeline for augmented co-expression analysis
Platform for integrative analysis of omics data
Platform for integrative analysis of omics data
Plot Gene Ontology and KEGG pathway Annotation and Abundance
PoTRA: Pathways of Topological Rank Analysis
PoTRA: Pathways of Topological Rank Analysis
PoTRA: Pathways of Topological Rank Analysis
Prediction of pathway-related protein-protein interaction networks
Probabilistic combinatorial nested effects model
Provides shiny components to visualize multilGSEA results
Random walk with restart on multiplex and heterogeneous Networks
Random walk with restart on multiplex and heterogeneous Networks
Reactome Pathway Analysis
Reactome Pathway Analysis
Reduce + Visualize GO
Reduce + Visualize GO
Reduce + Visualize GO
Reduce + Visualize GO
Reduce + Visualize GO
Render molecular pathways
Reproducible GSEA Benchmarking
Reproducible GSEA Benchmarking
R Interface with InterMine-Powered Databases
R Interface with InterMine-Powered Databases
R Interface with InterMine-Powered Databases
R Interface with InterMine-Powered Databases
RNASeqR: an R package for automated two-group RNA-Seq analysis workflow
RNASeqR: an R package for automated two-group RNA-Seq analysis workflow
RNASeqR: an R package for automated two-group RNA-Seq analysis workflow
R package implementing the Cytoscape Exchange (CX) format
R support for SBML, using libsbml
"SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways"
"SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways"
SBML-R Interface and Analysis Tools
SBML-R Interface and Analysis Tools
Seamless navigation through combined results of set-based and network-based enrichment analysis
Seamless navigation through combined results of set-based and network-based enrichment analysis
signet: Selection Inference in Gene NETworks
signet: Selection Inference in Gene NETworks
Significance Analysis of Function and Expression
Significance Analysis of Function and Expression
Single-Cell Operation for Neat Enrichment
ssPATHS: Single Sample PATHway Score
ssPATHS: Single Sample PATHway Score
ssPATHS: Single Sample PATHway Score
StarBioTrek
StarBioTrek
StarBioTrek
statistical analysis and visualization of functional profiles for genes and gene clusters
statistical analysis and visualization of functional profiles for genes and gene clusters
statistical analysis and visualization of functional profiles for genes and gene clusters
statistical analysis and visualization of functional profiles for genes and gene clusters
Statistical Analysis of the GeneChip
Statistics for Integrative Genomics Analyses in R
Take command of set enrichment analyses through a unified interface.
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data
"TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data"
"TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data"
Testing Groups of Covariates/Features for Association with a Response Variable, with Applications to Gene Set Testing
Testing Groups of Covariates/Features for Association with a Response Variable, with Applications to Gene Set Testing
The package can identify the dysregulated KEGG pathways based on global influence from the internal effect of pathways and crosstalk between pathways.
The package can identify the dysregulated KEGG pathways based on global influence from the internal effect of pathways and crosstalk between pathways.
The package can implement the network-based metabolite pathway identification of pathways.
Time sensitive microRNA-mRNA integration, analysis and network generation tool
Time sensitive microRNA-mRNA integration, analysis and network generation tool
Tools for Connectivity Map-like analyses
Tools For Manipulating FOBI Ontology
Tools For Manipulating FOBI Ontology
Tools For Manipulating FOBI Ontology
Tools for manipulating GO and microarrays
Tools for manipulating GO and microarrays
Topology-based pathway analysis of RNA-seq data
Topology-based pathway analysis of RNA-seq data
Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data
Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data
Training of logical models from indirect measurements of perturbation experiments
Training of logical models from indirect measurements of perturbation experiments
Transcriptomic Ovarian Cancer Datasets
Transcriptomic Ovarian Cancer Datasets
Uses Brown's method to combine p-values from dependent tests
Visualise microarray and RNAseq data using gene ontology annotations
Visualise microarray and RNAseq data using gene ontology annotations
Visualise microarray and RNAseq data using gene ontology annotations
Visualise microarray and RNAseq data using gene ontology annotations
Visualization of Functional Enrichment Result
Visualization of Functional Enrichment Result
Visualization of Functional Enrichment Result
Visualizations of expressionSet Bioconductor object
Visualize all edges within a KEGG pathway and overlay LINCS data
Visualize all edges within a KEGG pathway and overlay LINCS data
Visualize all edges within a KEGG pathway and overlay LINCS data [option]