Biological pathway analysis software tools and databases

Pathway analysis applications

Biological pathway analysis software tools and databases

Most Recent Tools

CYRENE
Desktop

CYRENE

Focuses on the study of cis-regulatory genomics and gene regulatory networks.…

Focuses on the study of cis-regulatory genomics and gene regulatory networks. The CYRENE Project has three components: a cisGRN-Lexicon, a cisGRN-Browser, and the Virtual Sea Urchin software system…

APPAGATO
Desktop

APPAGATO APproximate PArallel and stochastic GrAph querying Tool

Finds approximate occurrences of a query network in biological networks.…

Finds approximate occurrences of a query network in biological networks. APPAGATO handles node, edge and node label mismatches. It applies to large networks and provides high performance as well as…

NARROMI
Desktop

NARROMI

Improves the accuracy of gene regulatory network (GRN) inference by combining…

Improves the accuracy of gene regulatory network (GRN) inference by combining ordinary differential equation-based recursive optimization (RO) and information theory-based mutual information (MI).…

SIMoNe
Desktop

SIMoNe Statistical Inference for MOdular NEtworks

Enables inference of gene-regulatory networks based on partial correlation…

Enables inference of gene-regulatory networks based on partial correlation coefficients from microarray experiments. SIMoNe is based on a Gaussian graphical model and estimates non-zero entries of…

Most Popular Tools

CMGRN
Web

CMGRN Constructing Multilevel Gene Regulatory Networks

An integrative web server to unravel hierarchical interactive networks at…

An integrative web server to unravel hierarchical interactive networks at different regulatory levels. The developed method used the Bayesian network modeling to infer causal interrelationships among…

ProteinLounge
Web

ProteinLounge

Develops many interactive web-based databases and software to help the…

Develops many interactive web-based databases and software to help the life-scientists understand the complexity of systems biology. Systems biology efforts focus on understanding cellular networks,…

BiGG Models
Data

BiGG Models

A completely redesigned Biochemical, Genetic and Genomic knowledge base. BiGG…

A completely redesigned Biochemical, Genetic and Genomic knowledge base. BiGG Models contains more than 75 high-quality, manually-curated genome-scale metabolic models. On the website, users can…

NCG
Data

NCG Network of Cancer Genes

A manually curated repository of cancer genes derived from the scientific…

A manually curated repository of cancer genes derived from the scientific literature. NCG release 5.0 (August 2015) collects 1571 cancer genes from 175 published studies that describe 188 mutational…

Curators for Pathway analysis

  • Gary Bader's avatar image
    Gary Bader
    Department of Computer Science,…
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