Biocview "Pathways"

Access Pathways from Multiple Databases Through BioPAX and Pathway Commons

Activity and Diversity Analysis Module Graphical User Interface

ADAM: Activity and Diversity Analysis Module

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 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 integrated analysis package of miRNA and mRNA expression data

An interface to the Semantic MEDLINE database

Annotation for microarrays

Annotation tools for Affymetrix biological metadata

An R Package For Geneset Enrichment Workflows

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

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 pathway based data integration and visualization

A unified interface to a plethora of gene set enrichment analysis methods

A universal enrichment tool for interpreting omics data

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

BioMM: Biological-informed Multi-stage Machine learning framework for phenotype prediction using omics data

BLMA: A package for bi-level meta-analysis

Build Annotation From Online Database

Category Analysis

CHRONOS: A time-varying method for microRNA-mediated sub-pathway enrichment analysis

Client for GREAT Analysis

Client-side REST access KEGG

Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG)

CNCDriver

Codon Usage Analysis and Prediction of Gene Expressivity

co-expressed gene-set enrichment analysis

Co-expression Modules identification Tool

Combining GSEA-based pathway enrichment with multi omics data integration

CompositeDriver

Computation of functional similarities between GO terms and gene products; GO enrichment analysis

Computing multi-omics driven similarity scores between patient tumor samples and cell lines for personalized medicine

Conducts pathway test of metabolomics data using a weighted permutation test

COSMOS (Causal Oriented Search of Multi-Omic Space)

Creation and Analysis of Pathway Expression Profiles (PEPs)

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

Detection of clonally exclusive gene or pathway pairs in a cohort of cancer patients

Detection of miRNAs that regulate interacting groups of pathways

dgeAnalysis

Discriminant Analysis for Evolutionary Inference

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

Efficient, Scalable, and Reproducible Enrichment Workflows

Empirical Analysis of Digital Gene Expression Data in R

Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional Enrichment Analysis

Enrichment Analysis using Multiple Ontologies and False Discovery Rate

Ensemble of Gene Set Enrichment Analyses

epiNEM

ESEA: Discovering the Dysregulated Pathways based on Edge Set Enrichment Analysis

Estimate Systems Immune Response from RNA-seq 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

FCBF-based Co-Expression Networks for Single Cells

fedupShiny

Finding an Active Metabolic Module in Atom Transition Network

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

Functional analysis of metabolic and transcriptomic data

Functional Enrichment analysis

Functional Gene Networks derived from biological enrichment analyses

Functional similarities

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 Enrichment Analysis with Networks

Geneset enrichment based on InterPro domain signatures

Gene Set Enrichment Meta-Analysis

Gene-set Enrichment with Regularized Regression

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

GO-function: deriving biologcially relevant functions from statistically significant functions

goProfiles: an R package for the statistical analysis of functional profiles

GO-terms Semantic Similarity Measures

GRAPH Interaction from pathway Topological Environment

graph support for KO, KEGG Orthology

GREAT Analysis - Functional Enrichment on Genomic Regions

HiPathia: High-throughput Pathway Analysis

Identification of candidate causal perturbations from differential gene expression data

Identify oncogenes and tumor suppressor genes from omics data

Individualized Multi-Omic Pathway Deviation Scores Using Multiple Factor Analysis

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 Pathway Analysis with Modern PCA Methodology and Gene Selection

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 of RNA-seq experiments through robust, efficient comparison to public databases

iPath pipeline for detecting perturbed pathways at individual level

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

KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline

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

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 the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor Landscape

MethylMix: Identifying methylation driven cancer genes

'MicroRNA' Set Enrichment Analysis

miRNApath: Pathway Enrichment for miRNA Expression Data

Mixture Nested Effects Models

Model-based gene set analysis

Multi Dimensional Gene Set Analysis.

Multi-omics Classification, Functional Enrichment and Network Inference analysis

Multivariate and directional gene set testing

Murine Palate miRNA Expression Analysis

NDEx R client library

netboxr

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

Overlay omics data onto SBGN pathway diagram

Package for CTDbase data query, visualization and downstream analysis

PaIRKAT

Pathway Association Study Tool (PAST)

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

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

Platform for integrative analysis of omics data

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

Plot Gene Ontology and KEGG pathway Annotation and Abundance

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

Reactome Pathway Analysis

Reduce + Visualize GO

Render molecular pathways

Reproducible GSEA Benchmarking

R Interface with InterMine-Powered Databases

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"

SBML-R Interface and Analysis Tools

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

Shiny GATOM

Signature Overrepresentation Analysis

signet: Selection Inference in Gene NETworks

Significance Analysis of Function and Expression

Single-Cell Operation for Neat Enrichment

ssPATHS: Single Sample PATHway Score

StarBioTrek

statistical analysis and visualization of functional profiles for genes and gene clusters

Statistical Analysis of the GeneChip

Statistical inference based on the Sorensen-Dice dissimilarity and the Gene Ontology (GO)

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

"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

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

Tools for Connectivity Map-like analyses

Tools for manipulating GO and microarrays

Tools for Manipulating the FOBI Ontology

tool to run PHONEMeS on phosphoproteomic 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 logical models from indirect measurements of perturbation experiments

Transcriptomic Ovarian Cancer Datasets

Untargeted LC-MS data annotation

Uses Brown's method to combine p-values from dependent tests

Visualise microarray and RNAseq data using gene ontology annotations

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 [option]

Weighting protein-protein interactions

Wrapping functions for vissE server to use

Biocview "Pathways"

R Package Documentation

Browse R Packages

We want your feedback!