Biocview "NetworkEnrichment"

Access Pathways from Multiple Databases Through BioPAX and Pathway Commons

Affected pathway ranking in differential gene expression analysis

Analysis of co-regulation and inference of 'dual regulons'

analysis of co-regulatory network motifs and inference of 'dual regulons'.

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

Candidate Gene Miner

Co-expression Modules identification Tool

CoRegNet : reconstruction and integrated analysis of co-regulatory networks

DeMAND

DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq expression experiments

Differentially Expressed Gene-Gene pairs

Enrichment Approach to Predict Which Transcription Factors are Regulated

Ensemble of Gene Set Enrichment Analyses

Environment for Gene Expression Searching Combined with Functional Enrichment Analysis

Extending guilt by association by degree

FCBF-based Co-Expression Networks for Single Cells

fedupShiny

Fisher's Test for Enrichment and Depletion of User-Defined Pathways

From functional enrichment results to biological networks

Functional Gene Networks derived from biological enrichment analyses

Functional similarities

GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, mRNA, and miRNA data in GDC

Gene regulator enrichment analysis

Gene Set Enrichment Analysis with Networks

HTSanalyzeR2: An R package for functional annotation, network analysis and time series analysis of high-throughput data

Identification and analysis of miRNA sponge interaction networks and modules

Identification and analysis of miRNA sponge regulation

Identification of Functional Epigenetic Modules

Identifying genetic trait/phenotype relevant cell type/state at single cell resolution

Identify oncogenes and tumor suppressor genes from omics data

Inference of Genetic Variants Driving Cellular Phenotypes

Inferring functionally related proteins using protein interaction networks

Interaction Based Homogeneity for Evaluating Gene Lists

Interpretation and enrichment for metabolomics data

Metabolite Set Enrichment Analysis (MSEA)

miRNApath: Pathway Enrichment for miRNA Expression Data

Motif Analysis In Gene Regulatory Networks

Multi Omic Master Regulator Analysis

netboxr

Network-based Gene Prioritization Analysis (NetGPA)

Network-based pathway over-representation analysis (NetORA)

Package for CTDbase data query, visualization and downstream analysis

Pathway Enrichment Analysis Based on Bayesian Network

Pathway Enrichment Based on Differential Causal Effects

Pathway enrichment using a regularized regression approach

PaxtoolsR: Access Pathways from Multiple Databases through BioPAX and Pathway Commons

Pipeline for augmented co-expression analysis

plot bayesian network inferred from gene expression data based on enrichment analysis results

Rapid Integration of Term Annotation and Network resources

Reproducible GSEA Benchmarking

Routines for the functional analysis of biological networks

RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons

Seamless navigation through combined results of set-based and network-based enrichment analysis

signet: Selection Inference in Gene NETworks

Significance-based Modules Integrating the Transcriptome and Epigenome

Spatial Analysis of Network Associations

Survival analysis using transcriptional networks inferred by the RTN package

Time-course differential gene expression data analysis using spline regression models followed by gene association network reconstruction

Topology-based pathway analysis of RNA-seq data

Two-sample tests on a graph

VirtUaL ChIP-Seq data Analysis using Networks

Virtual Inference of Protein-activity by Enriched Regulon analysis

Visualising Set Enrichment Analysis Results

Biocview "NetworkEnrichment"

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