Solid tumor samples typically contain multiple distinct clonal populations of cancer cells, and also stromal and immune cell contamination. A majority of the cancer genomics and transcriptomics studies do not explicitly consider genetic heterogeneity and impurity, and draw…
Desktop app
G T A T C G C T A ABSOLUTE ABSOLUTE

ABSOLUTE

Infers tumor purity and malignant cell ploidy directly from analysis of somatic…

Infers tumor purity and malignant cell ploidy directly from analysis of somatic DNA alterations. ABSOLUTE can detect subclonal heterogeneity, somatic homozygosity, and calculate statistical…

Desktop app
G T A T C G C T A Expanding Ploidy and… Expanding Ploidy and Allele Frequency on Nested…

ExPANdS Expanding Ploidy and Allele Frequency on Nested Subpopulations

Characterizes coexisting subpopulations in a single tumor sample using copy…

Characterizes coexisting subpopulations in a single tumor sample using copy number and allele frequencies derived from exome- or whole genome sequencing input data. The model detects coexisting…

Desktop app
G T A T C G C T A CNAnorm CNAnorm

CNAnorm

A normalization method for copy number aberration in cancer samples. CNAnorm…

A normalization method for copy number aberration in cancer samples. CNAnorm performs ratio, GC content correction and normalization of data obtained using very low coverage (one read every…

Desktop app
G T A T C G C T A Canopy Canopy

Canopy

A statistical framework and computational procedure for identifying the…

A statistical framework and computational procedure for identifying the sub-populations within a tumor, determining the mutation profiles of each subpopulation, and inferring the tumor's…

Desktop app
G T A T C G C T A Computational… Computational Pathogen Sequence IDentification

CaPSID Computational Pathogen Sequence IDentification

Identifies, queries and visualizes both exogenous and endogenous pathogen…

Identifies, queries and visualizes both exogenous and endogenous pathogen nucleotide sequences in tumor genomes and transcriptomes. CaPSID integrates a high-performance computational pipeline for…

Desktop app
G T A T C G C T A QuantumClone QuantumClone

QuantumClone

Clusters variants into clones. QuantumClone applies an expectation-maximization…

Clusters variants into clones. QuantumClone applies an expectation-maximization (EM) algorithm and allows for accurate inference of clonal structure using Variant Allele Frequencies (VAFs) from one…

Desktop app
G T A T C G C T A Genomic Rearrangement… Genomic Rearrangement Assembly For Tumours

GRAFT Genomic Rearrangement Assembly For Tumours

A technique to help reconstruct the history of rearrangements responsible for…

A technique to help reconstruct the history of rearrangements responsible for cancer genome karyotypes. This uses allelic copy number segmentation, rearrangements, and somatic single-nucleotide…

Desktop app
G T A T C G C T A qpure qpure

qpure

Estimates tumour cellularity in samples to be used for cancer genomic studies…

Estimates tumour cellularity in samples to be used for cancer genomic studies where the presence of normal tissue in the tumor sample can significantly affect downstream analyses. qpure is an…

Desktop app
G T A T C G C T A Muttree Muttree

Muttree

Infers an evolutionary mutation tree based on single cell sequencing data.…

Infers an evolutionary mutation tree based on single cell sequencing data. Muttree differs from traditional phylogenetic tree approaches in that mutation tree directly describes temporal order…

Desktop app
G T A T C G C T A Somatic Phylogeny… Somatic Phylogeny Reconstruction Using…

SPRUCE Somatic Phylogeny Reconstruction Using Combinatorial Enumeration

Infers a multi-state perfect phylogeny describing the evolutionary history of…

Infers a multi-state perfect phylogeny describing the evolutionary history of the somatic mutations (Single-Nucleotide Variations (SNV)s and Copy-Number Aberrations (CNAs)) of a tumor given…

Desktop app
G T A T C G C T A MuSE MuSE

MuSE

A somatic point mutation caller for tumor-normal paired samples in…

A somatic point mutation caller for tumor-normal paired samples in next-generation sequencing data. MuSE models the evolution of the reference allele to the allelic composition of the matched tumor…

Desktop app
G T A T C G C T A BitPhylogeny BitPhylogeny

BitPhylogeny

A probabilistic framework to reconstruct intra-tumor evolutionary pathways. The…

A probabilistic framework to reconstruct intra-tumor evolutionary pathways. The statistical model is based on simultaneously assigning markers of evolution to clones, which are represented as both…

Desktop app
G T A T C G C T A Canvas Canvas

Canvas

A tool for identification of copy number changes from diverse sequencing…

A tool for identification of copy number changes from diverse sequencing experiments including whole-genome matched tumor-normal and single-sample normal re-sequencing, as well as whole-exome matched…

Desktop app
G T A T C G C T A BubbleTree BubbleTree

BubbleTree

An intuitive representation of purity, allele-specific copy number, and…

An intuitive representation of purity, allele-specific copy number, and clonality for human tumor specimens. BubbleTree displays the clonal composition within a tumor at the genomic segment level…

Desktop app
G T A T C G C T A SCUnmix SCUnmix

SCUnmix

A method for deconvoluting mixtures of genomic data with the goal of more…

A method for deconvoluting mixtures of genomic data with the goal of more accurately reconstructing cellular progression processes from bulk tumor genomic data. The method is designed to take better…

Desktop app
G T A T C G C T A cancerTiming cancerTiming

cancerTiming

A maximum-likelihood estimation procedure that fully accounts for sequencing…

A maximum-likelihood estimation procedure that fully accounts for sequencing variability and show that it outperforms the partial maximum-likelihood estimation method. A Bayesian estimation procedure…

Desktop app
G T A T C G C T A cloneHD cloneHD

cloneHD

A software tool for reconstructing the subclonal structure of a population from…

A software tool for reconstructing the subclonal structure of a population from short-read sequencing data. Read depth data, B-allele count data and somatic nucleotide variant (SNV) data can be used…

Desktop app
G T A T C G C T A FISHtrees FISHtrees

FISHtrees

A framework for inferring models of tumor progression from single-cell gene…

A framework for inferring models of tumor progression from single-cell gene copy number data, including variable rates for different gain and loss events. Application of FISHtrees to real cervical…

Desktop app
G T A T C G C T A Minimum Event… Minimum Event Distance for Intra-tumour…

MEDICC Minimum Event Distance for Intra-tumour Copy-number Comparisons

A method for phylogenetic reconstruction and heterogeneity quantification based…

A method for phylogenetic reconstruction and heterogeneity quantification based on a minimum event distance for intra-tumour copy-number comparisons. Given multiple such evolutionarily-related…

Desktop app
G T A T C G C T A TuMult TuMult

TuMult

A computational method for reconstructing the sequence of copy number changes…

A computational method for reconstructing the sequence of copy number changes driving carcinogenesis, based on the analysis of several tumor samples from the same patient. TuMult is a valuable tool…

Desktop app
G T A T C G C T A AncesTree AncesTree

AncesTree

Infers the clonal evolution and tumor composition, including mixing fractions,…

Infers the clonal evolution and tumor composition, including mixing fractions, of a tumor from multi-sample DNA sequence data. AncesTree is better able to identify ancestral relationships between…

Desktop app
G T A T C G C T A Lineage Inference for… Lineage Inference for Cancer Heterogeneity and…

LICHeE Lineage Inference for Cancer Heterogeneity and Evolution

Automates the phylogenetic inference of cancer progression from multiple…

Automates the phylogenetic inference of cancer progression from multiple somatic samples. LICHeE uses variant allele frequencies of somatic single nucleotide variants obtained by deep sequencing to…

Desktop app
G T A T C G C T A Subcloneseeker Subcloneseeker

Subcloneseeker

Examines somatic variation events (such as copy number changes, loss of…

Examines somatic variation events (such as copy number changes, loss of heterozygosity, or point mutations) in order to identify the underlying subclone structure, i.e. the subclones including the…

Desktop app
G T A T C G C T A CNALR CNALR

CNALR

An R package to perform a stratification of tumour subtypes based on copy…

An R package to perform a stratification of tumour subtypes based on copy number alteration profiles using next-generation sequence data. CNALR exhibits the best agreement in the prediction between…

Desktop app
G T A T C G C T A Clomial Clomial

Clomial

A generative binomial model that incorporates information from multiple…

A generative binomial model that incorporates information from multiple sections from a single tumor at a single time point to infer the frequencies and genotypes for a specified number of clones. An…

Desktop app
G T A T C G C T A PhyloWGS PhyloWGS

PhyloWGS

A method that can be applied to WGS data from one or more tumor samples to…

A method that can be applied to WGS data from one or more tumor samples to reconstruct complete genotypes of these subpopulations based on variant allele frequencies (VAFs) of point mutations and…

Desktop app
G T A T C G C T A Clonality Inference… Clonality Inference in Tumors Using Phylogeny

CITUP Clonality Inference in Tumors Using Phylogeny

A combinatorial method that infers clonal populations and their frequencies…

A combinatorial method that infers clonal populations and their frequencies while satisfying phylogenetic constraints and is able to exploit data from multiple samples. Using simulated datasets and…

Desktop app
G T A T C G C T A Bayclone Bayclone

Bayclone

An allocation model to describe tumor heterogeneity (TH) using next-generation…

An allocation model to describe tumor heterogeneity (TH) using next-generation sequencing (NGS) data. Taking a Bayesian approach, the Indian buffet process (IBP) is extended to define a class of…

Desktop app
G T A T C G C T A CLONality Estimate in… CLONality Estimate in Tumors

CLONET CLONality Estimate in Tumors

Cancer arises from initiating cells (clones) that undergo intense evolutionary…

Cancer arises from initiating cells (clones) that undergo intense evolutionary selection during disease progression and can be widely altered during treatment. The tumor cell evolutionary process may…

Desktop app
G T A T C G C T A Sequenza Sequenza

Sequenza

A software package that uses paired tumor-normal DNA sequencing data to…

A software package that uses paired tumor-normal DNA sequencing data to estimate tumor cellularity and ploidy, and to calculate allele-specific copy number profiles and mutation profiles. Comparison…

Desktop app
G T A T C G C T A Binary Tree Partition Binary Tree Partition

rec-BTP Binary Tree Partition

A combinatorial formulation of the problem of constructing the subpopulations…

A combinatorial formulation of the problem of constructing the subpopulations of tumor cells from the variant allele frequencies of somatic mutations. BTP outperforms existing clustering approaches…

Desktop app
G T A T C G C T A Tree Approach Tree Approach

TrAp Tree Approach

An evolutionary framework for deconvolving data from a single genome-wide…

An evolutionary framework for deconvolving data from a single genome-wide experiment to infer the composition, abundance and evolutionary paths of the underlying cell subpopulations of a tumor. TrAp…

Desktop app
G T A T C G C T A PhyloSub PhyloSub

PhyloSub

A statistical model that infers the phylogeny and genotype of the major…

A statistical model that infers the phylogeny and genotype of the major subclonal lineages represented in the population of cancer cells. It uses a Bayesian nonparametric prior over trees that groups…

Desktop app
G T A T C G C T A TITAN TITAN

TITAN

A tool for predicting subclonal copy number alterations (CNA) and loss of…

A tool for predicting subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) from tumour whole genome sequencing data. It infers the clonal cluster of events along with their…

Desktop app
G T A T C G C T A SciClone SciClone

SciClone

An R package for inferring the subclonal architecture of tumors.

An R package for inferring the subclonal architecture of tumors.

Desktop app
G T A T C G C T A PurBayes PurBayes

PurBayes

An MCMC-based algorithm that uses next-generation sequencing data to estimate…

An MCMC-based algorithm that uses next-generation sequencing data to estimate tumor purity and clonality for paired tumor-normal data.

Desktop app
G T A T C G C T A PurityEst PurityEst

PurityEst

A computational tool for estimating purity of human tumor samples using…

A computational tool for estimating purity of human tumor samples using next-generation sequencing data.

Desktop app
G T A T C G C T A PyLOH PyLOH

PyLOH

A model to resolve the identifiability problem by integrating two types of…

A model to resolve the identifiability problem by integrating two types of sequencing information - somatic copy number alterations and loss of heterozygosity.

Desktop app
G T A T C G C T A Tumor Heterogeneity… Tumor Heterogeneity Analysis

THetA Tumor Heterogeneity Analysis

An algorithm that estimates the tumor purity and clonal/subclonal copy number…

An algorithm that estimates the tumor purity and clonal/subclonal copy number aberrations directly from high-throughput DNA sequencing data. THetA successfully estimates normal admixture and recovers…

Desktop app
G T A T C G C T A PyClone PyClone

PyClone

A tool for inferring the cellular frequency of point mutations from deeply…

A tool for inferring the cellular frequency of point mutations from deeply sequenced data. The model supports simultaneous analysis of multiple related samples and infers clusters of mutations whose…

Desktop app
G T A T C G C T A deepSNV deepSNV

deepSNV

Detection of subclonal SNVs in deep sequencing experiments.

Detection of subclonal SNVs in deep sequencing experiments.

Desktop app
G T A T C G C T A AbsCN-seq AbsCN-seq

AbsCN-seq

A simple and robust algorithm to infer purity, ploidy and absolute copy numbers…

A simple and robust algorithm to infer purity, ploidy and absolute copy numbers in whole numbers for tumor cells from sequencing data. A simulation study shows that estimates have reasonable…

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