Cancer can be a result of accumulation of different types of genetic mutations such as copy number aberrations. The data from tumors are cross-sectional and do not contain the temporal order of the genetic events. Finding the order in which the genetic events have occurred and…
Desktop app
TiMEx TiMEx

TiMEx

A generative probabilistic model for detecting patterns of various degrees of…

A generative probabilistic model for detecting patterns of various degrees of mutual exclusivity across genetic alterations, which can indicate pathways involved in cancer progression. TiMEx…

Desktop app
deconstructSigs deconstructSigs

deconstructSigs

Allows the identification of mutational signatures within a single tumor…

Allows the identification of mutational signatures within a single tumor sample. The deconstructSigs approach determines the linear combination of pre-defined signatures that most accurately…

Web app
Cellular Potts Model… Cellular Potts Model Cytoscape

CPM-Cytoscape Cellular Potts Model Cytoscape

A comprehensive and expandable simulation tool to visualizing tumor growth.…

A comprehensive and expandable simulation tool to visualizing tumor growth. CPM-Cytoscape offers the advantage of a user-friendly graphical interface with several manipulable input variables to…

Desktop app
Phylogenetic tree… Phylogenetic tree Clustering

phyC Phylogenetic tree Clustering

A clustering method for cancer sub-clonal evolutionary trees, in which…

A clustering method for cancer sub-clonal evolutionary trees, in which sub-groups of the trees are identified based on topology and edge length attributes. phyC can detect true clusters with…

Desktop app
TRanslational ONCOlogy TRanslational ONCOlogy

TRONCO TRanslational ONCOlogy

An open-source R package that implements the state-of-the-art algorithms for…

An open-source R package that implements the state-of-the-art algorithms for the inference of cancer progression models from (epi)genomic mutational profiles. TRONCO can be used to extract…

HPVbase HPVbase

HPVbase

A comprehensive resource for three major efficacious cancer biomarkers i.e.…

A comprehensive resource for three major efficacious cancer biomarkers i.e. integration and breakpoint events, human papillomaviruses (HPVs) methylation patterns and HPV mediated aberrant expression…

Desktop app
CAncer PRogression… CAncer PRogression Inference

CAPRI CAncer PRogression Inference

Relies on a scoring method based on a probabilistic theory developed by Suppes,…

Relies on a scoring method based on a probabilistic theory developed by Suppes, coupled with bootstrap and maximum likelihood inference. The resulting algorithm is efficient, achieves high accuracy…

Desktop app
Continuous Time… Continuous Time Conjunctive Bayesian Networks

CT-CBN Continuous Time Conjunctive Bayesian Networks

A specific probabilistic graphical model for the accumulation of mutations and…

A specific probabilistic graphical model for the accumulation of mutations and their interdependencies. The Bayesian network models cancer progression by an explicit unobservable accumulation process…

Desktop app
Oncotree Oncotree

Oncotree

Estimating oncogenetic trees. Oncotree contains functions to construct and…

Estimating oncogenetic trees. Oncotree contains functions to construct and evaluate directed tree structures that model the process of occurrence of genetic alterations during carcinogenesis.

Desktop app
DiProg DiProg

DiProg

A software tool for learning disease progression networks by reducing to mixed…

A software tool for learning disease progression networks by reducing to mixed integer linear programming (MILP). In contrast to the semi-automatic method, DiProg is automatic and, therefore, needs…

Desktop app
hotmix hotmix

hotmix

This tool is used to generate hidden-variable oncogenetic trees (HOTs). The…

This tool is used to generate hidden-variable oncogenetic trees (HOTs). The trees are written using standard Newick notation, except that each vertex in the tree has a comment that describes the HOT…

Desktop app
Mtreemix Mtreemix

Mtreemix

A software package to estimate mixture models of mutagenetic trees from…

A software package to estimate mixture models of mutagenetic trees from observed cross-sectional data. Mutagenetic tree mixtures are probabilistic models that have been designed to describe…

Desktop app
oncomodel oncomodel

oncomodel

An approach for modelling the dependences between genetic changes in human…

An approach for modelling the dependences between genetic changes in human tumours. oncomodel computes probabilistic tree models for oncogenesis based on genetic data using maximum likelihood. In…

Desktop app
Rtreemix Rtreemix

Rtreemix

Offers an environment for estimating the mutagenetic trees mixture models from…

Offers an environment for estimating the mutagenetic trees mixture models from cross-sectional data and using them for various predictions. Rtreemix includes functions for fitting the trees mixture…

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