Software

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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.

 
 
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Sun Aug 28 22:38:01 CEST 2016
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