Biocview "Pathways"

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
A metagenomic pipeline for systems biology
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 integrated analysis package of miRNA and mRNA expression data
Annotation for microarrays
Annotation for microarrays
Annotation tools for Affymetrix biological metadata
Annotation tools for Affymetrix biological metadata
An R package for pathway analysis using topological information
An R package for pathway analysis using topological information
An R package to perform the network enrichment analysis (NEA).
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
Better prediction by use of co-data: Adaptive group-regularized ridge regression
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
BLMA: A package for bi-level meta-analysis
BLMA: A package for bi-level meta-analysis
BLMA: A package for bi-level meta-analysis
Calculates a global test for differential gene expression between groups
Calculates a global test for differential gene expression between groups
Category Analysis
Category Analysis
CHRONOS: A time-varying method for microRNA-mediated sub-pathway enrichment 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 for GREAT Analysis
Client-side REST access KEGG
Client-side REST access to KEGG
Client-side REST access to KEGG
Client-side REST access to KEGG
co-expressed gene-set enrichment analysis
co-expressed gene-set enrichment analysis
co-expressed gene-set enrichment analysis
Computation of functional similarities between GO terms and gene products; GO enrichment analysis
Computation of functional similarities between GO terms and gene products; GO enrichment analysis
Denoising Algorithm based on Relevance network Topology
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
DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq expression experiments
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
(Dynamic) Nested Effects Models and Deterministic Effects Propagation Networks to reconstruct phenotypic hierarchies
Ensemble of Gene Set Enrichment Analyses
Ensemble of Gene Set Enrichment Analyses
epiNEM
epiNEM
epiNEM
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
Fast Gene Set Enrichment Analysis
Fast Gene Set Enrichment Analysis
Fast Gene Set Enrichment Analysis
Functional Gene Networks derived from biological enrichment analyses
Functional Gene Networks derived from biological enrichment analyses
Functional similarities
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
Functions for Multinomial Occupancy Distribution
Generally Applicable Gene-set Enrichment for Pathway Analysis
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 methods for SNP association p-values that lie in genes in given gene sets
Geneset enrichment based on InterPro domain signatures
Geneset enrichment based on InterPro domain signatures
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
GO-function: deriving biologcially relevant functions from statistically significant functions
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
graph support for KO, KEGG Orthology
Identify oncogenes and tumor suppressor genes from omics data
Identify oncogenes and tumor suppressor genes from omics data
Identify oncogenes and tumor suppressor genes from omics data
Integrating microRNA expression into signaling pathways for pathway analysis
Integrating microRNA expression into signaling pathways for pathway analysis
Interactive Multi-Omics Cancers Data Visualization and Analysis
Interactive Multi-Omics Cancers Data Visualization and Analysis
Interactive Multi-Omics Cancers Data Visualization and Analysis
JODA algorithm for quantifying gene deregulation using knowledge
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
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
Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene, Pathway and Network Level
Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene, Pathway and Network Level
LiquidAssociation
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
Meta-analysis of high-throughput experiments using feature annotations
MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathways
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
'MicroRNA' Set Enrichment Analysis
miRNApath: Pathway Enrichment for miRNA Expression Data
miRNApath: Pathway Enrichment for miRNA Expression Data
Model-based gene set analysis
Model-based gene set analysis
Model-based gene set analysis
Multi Dimensional Gene Set Analysis.
Multi Dimensional Gene Set Analysis.
Multi Dimensional Gene Set Analysis.
Multivariate and directional gene set testing
Multivariate and directional gene set testing
Murine Palate miRNA Expression Analysis
Murine Palate miRNA Expression Analysis
NDEx R client library
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
Outlier profile and pathway analysis in R
Outlier profile and pathway analysis in R
Outlier profile and pathway analysis in R
Package for Topology-based Pathway Analysis of RNASeq data
Package for Topology-based Pathway Analysis of RNASeq data
Pathways from the NCI Pathways Database
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
PaxtoolsR: Access Pathways from Multiple Databases through BioPAX and Pathway Commons
Permutation approximation methods for gene set enrichment analysis (non-permutation GSEA)
Permutation approximation methods for gene set enrichment analysis (non-permutation GSEA)
Phenotype Consensus ANalysis (PCAN)
Phenotype Consensus ANalysis (PCAN)
Platform for integrative analysis of omics data
Platform for integrative analysis of omics data
Prediction of pathway-related protein-protein interaction networks
Prediction of pathway-related protein-protein interaction networks
Reactome Pathway Analysis
Reactome Pathway Analysis
Reactome Pathway Analysis
Render molecular pathways
Render molecular pathways
R Interface with InterMine-Powered Databases
R Interface with InterMine-Powered Databases
R Interface with InterMine-Powered Databases
R support for SBML, using libsbml
R support for SBML, using libsbml
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
Significance Analysis of Function and Expression
Significance Analysis of Function and Expression
StarBioTrek
StarBioTrek
StarBioTrek
StarTrek
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
Statistical Analysis of the GeneChip
Statistics for Integrative Genomics Analyses in R
Statistics for Integrative Genomics Analyses in R
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data
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"
"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 implement the network-based metabolite pathway identification of pathways.
Tools for Connectivity Map-like analyses
Tools for Connectivity Map-like analyses
Tools for manipulating GO and microarrays.
Tools for manipulating GO and microarrays.
training of logical models from indirect measurements of perturbation experiments
Uses Brown's method to combine p-values from dependent tests
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
Visualizations of expressionSet Bioconductor object
Visualizations of expressionSet Bioconductor object
Visualize all edges within a KEGG pathway and overlay LINCS data [option]
Visualize all edges within a KEGG pathway and overlay LINCS data [option]
Visualize all edges within a KEGG pathway and overlay LINCS data [option]
Visualize all edges within a KEGG pathway and overlay LINCS data [option]