# Navigation Area

# Software

# Main content

## CT-CBN

CT-CBN is a C program that implements algorithms for model selection and maximum likelihood parameter estimation of continuous time conjunctive Bayesian networks.

## bcbn

bcbn performs Bayesian inference of Conjunctive Bayesian Networks.

## BitPhylogeny

BitPhylogeny is a probabilistic framework for reconstructing intra-tumor phylogenies.

## BMix

BMix is a toolbox for analysing PAR-CLIP data and detecting T-to-C substitutions induced following RNA-protein cross-linking.

## deepSNV

deepSNV is an R package to test for low-frequency SNVs in deep sequencing experiments.

## Geno2pheno

Geno2pheno is a web server for the prediction of HIV phenotypic drug resistance and coreceptor usage from genotype.

## gespeR

gespeR is a R package to estimates gene-specific phenotypes from off-target confounded RNAi screens.

## HaploClique

HaploClique is a C++ software package that implements a method to reconstruct viral haplotypes and detect large insertions and deletions from NGS data.

## icbn

icbn is an R package for jointly estimating a conjunctive Bayesian network and an isotonic regression function on the induced genotype lattice from paired genotype-phenotype data.

## IGB

IGB is a R script for computing individualized genetic barrier.

## InDelFixer

InDelFixer is a java program to remove frame shift causing insertions or deletions from next-generation sequencing data.

## LIMEpi

LIMEpi is an R package that implements a latent interaction model-based SNP ranking and selection as the first stage of a two-stage epistasis detection.

## MC-CBN

MC-CBN performs large-scale inference on conjunctive Bayesian networks.

## MtreeHMM

MtreeHMM is a Perl program that implements an Expectation Maximization algorithm for estimating the parameters of the mutagenetic tree hidden Markov model from longitudinal clonal sequence data.

## Mtreemix

Mtreemix is a software package for learning and using mutagenetic trees, a family of graphical models for the accumulation of mutations.

## muex

muex is a statistical model of Mutual Exclusivity.

## MutationTiming

MutationTiming is a driver-passenger discrimination method which aims as identifying constrained cancer drivers.

## NEMix

NEMix is an R network inference model for learning nested effects models from single cell observations, accounting for noisy pathway activation.

## netprioR

netprioR is an R package for network-based integrative gene prioritisation.

## OTCBN

OTCBN is an R package for estimating a timed conjunctive Bayesian network from paired genotype-sampling time data.

## QuasiFit

QuasiFit is a Bayesian MCMC sampler that infers fitness from a dynamic equilibrium distribution.

## QuasiRecomb

QuasiRecomb is a java software to infer a viral quasispecies from Next Generation Sequencing (NGS) data.

## ROCR

ROCR is an R package for the visualization and ROC analysis of the performance of binary classifiers.

## SCITE

SCITE is a C++ software package for reconstructing mutation histories of tumours based on noisy single-cell sequencing data.

## ShoRAH

ShoRAH is a software package for inferring haplotypes and their frequencies from short sequence reads obtained from ultra-deep sequencing of a mixed sample.

## staRank

staRank is an R package for ranking variables according to their stability. Stability is estimated through boostrapping.

## TiMEx

TiMEx is a Bioconductor package implementing a waiting time model for mutually exclusive cancer alterations.