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Driver pathway identification software tools | Pathway analysis

It has been widely realized that pathways rather than individual genes govern the course of carcinogenesis. Therefore, discovering driver pathways is becoming an important step to understand the molecular mechanisms underlying cancer and design…
MUFFINN
Web
Desktop

MUFFINN MUtations For Functional Impact on Network Neighbors

A cancer gene prioritization method based on a pathway-centric analysis of…

A cancer gene prioritization method based on a pathway-centric analysis of mutation data. MUFFINN integrates mutational information for individual genes and their neighbors in co-functional networks.…

G T A T C G C T A
DrGaP
Desktop

DrGaP Driver Genes and Pathways

A powerful and flexible statistical framework for identifying driver genes and…

A powerful and flexible statistical framework for identifying driver genes and driver signaling pathways in cancer genome-sequencing studies. DrGaP is immediately applicable to cancer…

NBS
Desktop

NBS Network-Based Stratification

A method for stratification (clustering) of patients in a cancer cohort based…

A method for stratification (clustering) of patients in a cancer cohort based on genome scale somatic mutations measurements and a gene interaction network. We demonstrate NBS in ovarian, uterine and…

CoMEt
Desktop

CoMEt Combinations of Mutually Exclusive Alterations

Identifies combinations of alterations that exhibit a pattern of mutual…

Identifies combinations of alterations that exhibit a pattern of mutual exclusivity across individuals, often observed for alterations in the same pathway. CoMEt includes an exact statistical test…

oncoIMPACT
Desktop

oncoIMPACT

A data integration framework (OncoIMPACT) to nominate patient-specific driver…

A data integration framework (OncoIMPACT) to nominate patient-specific driver genes based on their phenotypic impact. Extensive in silico and in vitro validation helped establish OncoIMPACT's…

MEMCover
Algorithm

MEMCover Mutual Exclusivity Module Cover

Identifies a large number of subnetworks dysregulated across many cancer types.…

Identifies a large number of subnetworks dysregulated across many cancer types. MEMCover is an algorithm that uses a module cover optimization strategy to combine functional interactions, mutual…

DIGGIT
Desktop

DIGGIT Driver-gene Inference by Genetical-Genomic Information Theory

A package for the systematic discovery of genetic alterations that are causal…

A package for the systematic discovery of genetic alterations that are causal determinants of disease, by prioritizing genes upstream of functional disease drivers, within regulatory networks…

Mutex
Desktop

Mutex

A method for the identification of sets of mutually exclusive gene alterations…

A method for the identification of sets of mutually exclusive gene alterations in a given set of genomic profiles. We scan the groups of genes with a common downstream effect on the signaling…

Desktop

Cancer Correlation Clustering

Leverages mutual exclusivity of mutations, patient coverage and driver network…

Leverages mutual exclusivity of mutations, patient coverage and driver network concentration principles. To test C³, we performed a detailed analysis on TCGA breast cancer and glioblastoma data and…

PathScore
Web

PathScore

A web tool for identifying altered pathways in cancer data. PathScore…

A web tool for identifying altered pathways in cancer data. PathScore quantifies the level of enrichment of somatic mutations within curated pathways, applying a novel approach that identifies…

WeSME
Desktop

WeSME Weighted Sampling based Mutual Exclusivity

Estimates p-values of mutual exclusivity while taking into account mutation…

Estimates p-values of mutual exclusivity while taking into account mutation frequencies of patients. WeSME closely approximates the results of the permutation-based method and does so without using…

PheNetic eQTL
Desktop

PheNetic eQTL

A network-based analysis method that exploits public interactomics knowledge to…

A network-based analysis method that exploits public interactomics knowledge to analyze eQTL data sets. The results of PheNetic eQTL provide a simultaneous prioritization of driver mutations and an…

BeWith
Desktop

BeWith

Identifies multiple mutated modules displaying specific mutation patterns…

Identifies multiple mutated modules displaying specific mutation patterns between and within modules. BeWith is a general framework that reveals complex relations between mutual exclusivity,…

MCSS
Desktop

MCSS Minimum Cost Subset Selection

Finds multiple mutated driver pathways without the need to pre-specify a number…

Finds multiple mutated driver pathways without the need to pre-specify a number of pathways and/or a number of genes. MCSS is an algorithm developed for de novo discovery of driver mutation pathways…

Dendrix
Desktop

Dendrix De novo Driver Exclusivity

An algorithm for discovery of mutated driver pathways in cancer using only…

An algorithm for discovery of mutated driver pathways in cancer using only mutation data. Dendrix finds sets of genes, domains, or nucleotides whose mutations exhibit both high coverage and high…

DriverNet
Desktop

DriverNet

A package to predict functional important driver genes in cancer by integrating…

A package to predict functional important driver genes in cancer by integrating genome data (mutation and copy number variation data) and transcriptome data (gene expression data). The different…

SLAPenrich
Desktop

SLAPenrich Sample Level Analysis of Pathway Alteration Enrichments

A statistical method to identify pathway-level enrichments of genetic…

A statistical method to identify pathway-level enrichments of genetic alterations. SLAPenrich does not require the genes belonging to a given pathway to be statistically enriched among those altered…

DawnRank
Desktop

DawnRank

An R package that identifies personalized driver mutations for any given…

An R package that identifies personalized driver mutations for any given patient sample. Applications to TCGA datasets demonstrated the effectiveness of our method. We believe DawnRank complements…

VarWalker
Desktop

VarWalker

A mutation network method to prioritize driver genes in large scale cancer…

A mutation network method to prioritize driver genes in large scale cancer mutation data. VarWalker fits generalized additive models for each sample based on sample-specific mutation profiles and…

MUDPAC
Desktop

MUDPAC

Identifies collaborative driver pathways in cancer using a two-step approach:…

Identifies collaborative driver pathways in cancer using a two-step approach: mutational pathway enrichment analysis followed by greedy search for the collaborative driver pathways. In contrast to…

MDPFinder
Desktop

MDPFinder

Large-scale cancer genomics projects are providing a large volume of data about…

Large-scale cancer genomics projects are providing a large volume of data about genomic, epigenomic and gene expression aberrations in multiple cancer types. One of the remaining challenges is to…

PathScan
Desktop

PathScan

A pathway analysis tool using population data. The PathScan tool performs a…

A pathway analysis tool using population data. The PathScan tool performs a more sophisticated statistical analysis that considers these variables using Fisher-Lancaster theory, thus furnishing more…

CoMDP
Desktop

CoMDP Co-occurring Mutated Driver Pathways

A method for the de novo identification of co-occurring driver pathways in…

A method for the de novo identification of co-occurring driver pathways in cancer without any prior information beyond mutation profiles. Two possible properties of mutations that occurred in…

Multi-Dendrix
Desktop

Multi-Dendrix Multiple Pathways De novo Driver Exclusivity

An algorithm for the simultaneous identification of multiple driver pathways de…

An algorithm for the simultaneous identification of multiple driver pathways de novo in somatic mutation data from a cohort of cancer samples. Multi-Dendrix relies on two combinatorial properties of…

Oncodrive-CIS
Desktop

Oncodrive-CIS

Measures the in cis effect of copy number changes. Oncodrive-CIS a statistical…

Measures the in cis effect of copy number changes. Oncodrive-CIS a statistical framework that can be useful to identify genes involved in tumorigenesis due to CNAs. It may help to elucidate the role…

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