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Driver mutation prioritization software tools | Whole-genome sequencing data analysis

Distinguishing driver mutations from passenger mutations is critical to the understanding of the molecular mechanisms of carcinogenesis and for identifying prognostic and diagnostic markers as well as therapeutic targets. Source text: Zhang et al.,…
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Hotspots
Desktop

Hotspots

Identifies driver mutations, rather than driver genes. Hotspots is a…

Identifies driver mutations, rather than driver genes. Hotspots is a computational algorithm developed from a curated repository of cancer genome data consisting of the sequenced tumor exomes and…

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MutSig
Desktop

MutSig Mutation Significance

Analyzes lists of mutations discovered in DNA sequencing, to identify genes…

Analyzes lists of mutations discovered in DNA sequencing, to identify genes that were mutated more often than expected by chance given background mutation processes. MutSig was originally developed…

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PANTHER
Web

PANTHER Protein ANalysis THrough Evolutionary Relationships

A widely used online resource for comprehensive protein evolutionary and…

A widely used online resource for comprehensive protein evolutionary and functional classification, and includes tools for large-scale biological data analysis. The latest version of PANTHER, 10.0,…

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InVEx
Desktop

InVEx Introns Vs Exons

A permutation-based method for ascertaining genes with a somatic mutation…

A permutation-based method for ascertaining genes with a somatic mutation distribution showing evidence of positive selection for non-silent mutations. The method was developed for use in cancer…

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ActiveDriver
Desktop

ActiveDriver

A computational method for identifying 'active' sites in proteins…

A computational method for identifying 'active' sites in proteins (signalling sites, protein domains, regulatory motifs) that are specifically and significantly mutated in cancer genomes.…

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Oncodrive-fm
Desktop

Oncodrive-fm

An approach to uncover driver genes or gene modules. It computes a metric of…

An approach to uncover driver genes or gene modules. It computes a metric of functional impact using three well-known methods (SIFT, PolyPhen2 and MutationAssessor) and assesses how the functional…

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CHASM/SNV-Box
Desktop

CHASM/SNV-Box Cancer-specific High-throughput Annotation of Somatic Mutations

A software toolkit to prioritize SNVs based on their predicted contribution to…

A software toolkit to prioritize SNVs based on their predicted contribution to tumorigenesis. CHASM includes a database of pre-computed predictive features called SNVBox that facilitates rapid…

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MuSiC
Desktop

MuSiC Mutational Significance In Cancer

A set of tools aimed at determining the significance of somatic mutations…

A set of tools aimed at determining the significance of somatic mutations discovered within a given cohort of cancer samples, incorporating the cohort's alignment data, variant lists and any…

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HIT’nDRIVE
Desktop

HIT’nDRIVE

Analyzes genome and transcriptome data for identifying and prioritizing…

Analyzes genome and transcriptome data for identifying and prioritizing sequence altered genes as potential cancer drivers. HIT’nDRIVE is a combinatorial method that integrates patient-specific…

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CRAVAT
Web

CRAVAT Cancer-Related Analysis of Variants Toolkit

Performs cancer-related analysis of variants. CRAVAT returns mutation…

Performs cancer-related analysis of variants. CRAVAT returns mutation interpretations in a dynamic interactive web environment for sorting, visualizing and inferring mechanism. The software (i)…

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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…

Babelomics
Desktop
Web

Babelomics

A web application for the functional analysis of gene expression and genomic…

A web application for the functional analysis of gene expression and genomic data. Babelomics offers user-friendly access to a full range of methods that cover: (i) primary data analysis, (ii) a…

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RegNetDriver
Desktop

RegNetDriver

Infers the global impact of tumorigenic genetic and epigenetic alterations in…

Infers the global impact of tumorigenic genetic and epigenetic alterations in the tissue-specific network and identifies regulatory cancer drivers. RegNetDriver can be used to analyze other cancer…

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UNCeqR
Desktop

UNCeqR

Analyzes DNA-Whole Exome Sequencing (DNA-WES) and patient-matched RNA-seq to…

Analyzes DNA-Whole Exome Sequencing (DNA-WES) and patient-matched RNA-seq to detect somatic mutations genome-wide. UNCeqR is an algorithm that detects somatic mutations within exons based on input of…

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nsSNPAnalyzer
Web

nsSNPAnalyzer

A tool to predict whether a nonsynonymous single nucleotide polymorphism…

A tool to predict whether a nonsynonymous single nucleotide polymorphism (nsSNP) has a phenotypic effect. nsSNPAnalyzer also provides additional information about the SNP to facilitate the…

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PMut
Web
Desktop

PMut

Performs pathology predictions, gives access to a repository of pre-calculated…

Performs pathology predictions, gives access to a repository of pre-calculated predictions and generates and validates new predictors. PMut is a web-based tool that offers a generally trained…

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SNPs3D
Web

SNPs3D

Assigns molecular functional effects of non-synonymous SNPs based on structure…

Assigns molecular functional effects of non-synonymous SNPs based on structure and sequence analysis. There are three unique features of the SNPs3D resource. First, it is designed specifically for…

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SpacePAC
Desktop

SpacePAC

Identifies proteins with significant clusters. SpacePAC provides…

Identifies proteins with significant clusters. SpacePAC provides “localization” for mutational hotspots. It uses a three-step process to identify mutational clusters: (i) obtain the mutational…

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CLUMP
Desktop

CLUMP CLUstering by Mutation Position

Quantifies a significant difference in clustering between autosomal (AD) and…

Quantifies a significant difference in clustering between autosomal (AD) and autosomal recessive (AR) diseases. CLUMP is an unsupervised clustering of amino acid residue positions where variants…

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QuartPAC
Desktop

QuartPAC Quaternary Protein Amino acid Clustering

Provides a unique tool to identify mutational clustering while accounting for…

Provides a unique tool to identify mutational clustering while accounting for the complete folded protein quaternary structure. QuartPAC identifies non-random mutational clustering while utilizing…

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LowMACA
Desktop

LowMACA Low frequency Mutation Analysis via Consensus Alignment

A software for the identification of gain-of-function mutations in putative…

A software for the identification of gain-of-function mutations in putative oncogenic families, increasing the amount of information on functional domains and their possible role in cancer. In this…

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CLUMPS
Algorithm

CLUMPS CLUstering of Mutations in Protein Structures

Assesses the significance of mutational clustering in a given 3D structure.…

Assesses the significance of mutational clustering in a given 3D structure. CLUMPS is a statistical method that does not attempt to specify individual clusters but rather detects an overall…

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MEGSA
Desktop

MEGSA

A powerful and flexible framework for identifying mutually exclusive gene sets…

A powerful and flexible framework for identifying mutually exclusive gene sets (MEGS). MEGSA outperforms existing methods for de novo analyses and greatly improves the capability of recovering the…

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transFIC
Web

transFIC transformed Functional Impact score for Cancer

A method to transform functional impact scores taking into account the…

A method to transform functional impact scores taking into account the differences in basal tolerance to germline SNVs of genes that belong to different functional classes. This transformation allows…

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SAPRED
Web

SAPRED SAP Disease-Association Predictor

Offers the researchers an automatic pipeline to predict the disease-association…

Offers the researchers an automatic pipeline to predict the disease-association of single amino acid polymorphisms (SAPs). Through a strict protein-level 5-fold cross-validation, SAPRED attained an…

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SPARROW
Desktop

SPARROW SPARse selected expRessiOn regulators identified With penalized regression

A method to identify genes driving expression changes in cancer genome…

A method to identify genes driving expression changes in cancer genome evolution from genome-wide expression data. The SPARROW method uses a sparse regression methodology, variational Bayes spike…

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DMI
Desktop

DMI Driver Mutation Identification

Helps identify cancer-associated ‘driver' mutations from ‘passenger’…

Helps identify cancer-associated ‘driver' mutations from ‘passenger’ ones in a cancer genome. Generally, given a set of mutations, the DMI system could identify which of them are drivers,…

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NMC
Desktop

NMC Nonrandom Mutation Clustering

Identifies nonrandom mutation clustering without specifying the number of…

Identifies nonrandom mutation clustering without specifying the number of mutations or the cluster length. NMC is a statistical method written in R for detecting activating mutations in cancer. This…

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CanBind
Desktop
Web

CanBind

A computational pipeline for mapping large-scale cancer exome data across…

A computational pipeline for mapping large-scale cancer exome data across patients onto protein structures, and automatically extracting proteins with an enriched number of mutations affecting their…

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iSIMPRe
Desktop

iSIMPRe identification of SIgnificantly Mutated Protein Regions

Helps to interpret the effect of cancer mutations at the level of functional…

Helps to interpret the effect of cancer mutations at the level of functional regions. iSIMPRe is able to pinpoint proteins and protein regions that harbor a significant amount of cancer-related…

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ConsensusDriver
Desktop

ConsensusDriver

Provides users a framework to easily run a wide range of cancer driver…

Provides users a framework to easily run a wide range of cancer driver prediction methods on omics datasets and integrates results to obtain consensus predictions that have higher sensitivity and…

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Driver Genes
Desktop

Driver Genes

Allows integration of mutation, expression and functional data, a weighting…

Allows integration of mutation, expression and functional data, a weighting scheme for counting putative driver genes and a method for identifying drivers in a global and patient-specific manner…

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DEOD
Desktop

DEOD

A method for uncovering the dominant effects of cancer-driver genes based on a…

A method for uncovering the dominant effects of cancer-driver genes based on a partial covariance selection approach. Inspired by a convex optimization technique, DEOD estimates the dominant effects…

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MADGiC
Desktop

MADGiC Model-based Approach for identifying Driver Genes in Cancer

Identifying and prioritizing somatic mutations is an important and challenging…

Identifying and prioritizing somatic mutations is an important and challenging area of cancer research that can provide new insights into gene function as well as new targets for drug development.…

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e-Driver
Desktop

e-Driver

Identifies cancer driver genes based on linear annotations of biological…

Identifies cancer driver genes based on linear annotations of biological regions such as protein domains. e-Driver uses information on three-dimensional (3D) structures of the mutated proteins to…

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PRISMAD
Desktop
Web

PRISMAD Polymorphic Rates Indicate Somatic Mutations As Drives

The catalogue of tumour-specific somatic mutations (SMs) is growing rapidly…

The catalogue of tumour-specific somatic mutations (SMs) is growing rapidly owing to the advent of next-generation sequencing. Identifying those mutations responsible for the development and…

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GraphPAC
Desktop

GraphPAC Graph Protein Amino acid Clustering

Identifies mutational clusters of amino acids in a protein while utilizing the…

Identifies mutational clusters of amino acids in a protein while utilizing the proteins tertiary structure via a graph theoretical model. Using GraphPAC, we are able to detect novel clusters in…

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FATHMM
Desktop
Web

FATHMM Functional Analysis through Hidden Markov Models

A high-throughput web-server capable of predicting the functional consequences…

A high-throughput web-server capable of predicting the functional consequences of both coding variants, i.e. non-synonymous single nucleotide variants (nsSNVs), and non-coding variants. To facilitate…

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MutPrior
Algorithm

MutPrior

An approach to prioritize genes in a given caner. We hypothesize that a gene is…

An approach to prioritize genes in a given caner. We hypothesize that a gene is important for cancer if it has high functional impact mutations, is strategically important for network stability and…

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CancerMutationA…
Desktop

CancerMutationAnalysis

Implements gene and gene-set level analysis methods for somatic mutation…

Implements gene and gene-set level analysis methods for somatic mutation studies of cancer. The gene-level methods distinguish between driver genes (which play an active role in tumorigenesis) and…

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EnsembleGASVR
Desktop

EnsembleGASVR

An embedded classification technique, which combines an adaptive genetic…

An embedded classification technique, which combines an adaptive genetic algorithm (GA) with nu-support vector regression (nu-SVR), through an ensemble algorithmic framework. EnsembleGASVR predicts…

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ContrastRank
Web

ContrastRank

A method for prioritizing putative impaired genes in cancer. ContrastRank is…

A method for prioritizing putative impaired genes in cancer. ContrastRank is based on the comparison of exome sequencing data from different cohorts and can detect putative cancer driver genes. The…

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iPAC
Desktop

iPAC identification of Protein Amino acid Clustering

Identifies non-random somatic mutations in proteins while taking into account…

Identifies non-random somatic mutations in proteins while taking into account the three dimensional protein structure. By using the tertiary information, we are able to detect both novel clusters in…

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SomInaClust
Desktop

SomInaClust

A method that identifies cancer driver genes from whole exome/genome somatic…

A method that identifies cancer driver genes from whole exome/genome somatic mutation data. SomInaClust specifically prioritizes genes with a higher than expected number of clustering and/or…

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Ensemble…
Desktop

Ensemble classifier

An ensemble classifier (EC) machine learning method applied to the discovery of…

An ensemble classifier (EC) machine learning method applied to the discovery of driver candidates in breast and ovarian cancer samples from the Cancer Genome Atlas. EC integrates 10 classifiers that…

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OncodriveCLUST
Desktop

OncodriveCLUST

A method to identify genes with a significant bias towards mutation clustering…

A method to identify genes with a significant bias towards mutation clustering within the protein sequence. This method constructs the background model by assessing coding-silent mutations, which are…

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CanDrA
Desktop

CanDrA

Predicts cancer-type specific driver missense mutations based on a set of 95…

Predicts cancer-type specific driver missense mutations based on a set of 95 structural and evolutionary features computed by over 10 functional prediction algorithms such as CHASM, SIFT, and…

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libGenome
Desktop

libGenome

Allows users to make common operations on DNA and protein sequences. libGenome…

Allows users to make common operations on DNA and protein sequences. libGenome provides features for reading, writing, manipulating and annotating data.

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iCAGES
Web
Desktop

iCAGES integrated CAncer GEnome Score

Solves real-life problems by using patient’s genomic information. iCAGES…

Solves real-life problems by using patient’s genomic information. iCAGES comes up with a list of genes that are responsible for this particular patient, shedding light into personalized cancer…

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eFISMIC
Dataset

eFISMIC

A comprehensive database containing experimental evidence on the functional…

A comprehensive database containing experimental evidence on the functional impacts of somatic mutations detected in human cancer. eFISMIC is a valuable resource for storing and visualizing the…

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CanPredict
Web

CanPredict

Allows users to determine if particular changes are likely to be…

Allows users to determine if particular changes are likely to be cancer-associated. The impact of each change is measured using two known methods: Sorting Intolerant From Tolerant (SIFT) and the…

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ChroMoS
Web

ChroMoS Chromatin Modified SNPs

Combines genetic and epigenetic data with the goal of facilitating SNPs'…

Combines genetic and epigenetic data with the goal of facilitating SNPs' classification, prioritization and prediction of their functional consequences. ChroMoS uses a large database of SNPs and…

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MSEA
Desktop

MSEA Mutation Set Enrichment Analysis

By focusing on somatic SNVs and indels, we proposed two novel methods to detect…

By focusing on somatic SNVs and indels, we proposed two novel methods to detect candidate cancer genes whose somatic mutations tend to form mutation hotspot regions. The first method, MSEA-clust,…

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OncodriveROLE
Desktop
Web

OncodriveROLE

A machine learning-based approach that classifies driver genes according to…

A machine learning-based approach that classifies driver genes according to their role, using several properties related to the pattern of alterations across tumors. OncodriveROLE shows an accuracy…

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