Biological pathway analysis software tools and databases

Pathway analysis applications

Biological pathway analysis software tools and databases

Most Recent Tools

FCF
Desktop

FCF Flux Coupling Finder

Elucidates the topological and flux connectivity features of genome-scale…

Elucidates the topological and flux connectivity features of genome-scale metabolic networks and enables the global identification of blocked reactions, equivalent knockouts, and sets of affected…

SL Finder
Desktop

SL Finder

Proposes a targeted enumeration procedure for identification of synthetic…

Proposes a targeted enumeration procedure for identification of synthetic lethal (SL) genes or reactions using genome-scale metabolic models. SL Finder relies on the solution of a bilevel…

OptCom
Desktop

OptCom

Provides a comprehensive flux balance analysis framework for microbial…

Provides a comprehensive flux balance analysis framework for microbial communities. OptCom relies on a multi-level and multi-objective optimization formulation to properly describe trade-offs between…

pathifier
Desktop

pathifier

Infers pathway deregulation scores for each tumor sample on the basis of…

Infers pathway deregulation scores for each tumor sample on the basis of expression data. Pathifier is an algorithm that transforms gene-level information into pathway-level information, generating a…

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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