CT-CBN is a C program that implements algorithms for model selection and maximum likelihood parameter estimation of continuous time conjunctive Bayesian networks.
bcbn performs Bayesian inference of Conjunctive Bayesian Networks.
BitPhylogeny is a probabilistic framework for reconstructing intra-tumor phylogenies.
BMix is a toolbox for analysing PAR-CLIP data and detecting T-to-C substitutions induced following RNA-protein cross-linking.
deepSNV is an R package to test for low-frequency SNVs in deep sequencing experiments.
Geno2pheno is a web server for the prediction of HIV phenotypic drug resistance and coreceptor usage from genotype.
gespeR is a R package to estimates gene-specific phenotypes from off-target confounded RNAi screens.
HaploClique is a C++ software package that implements a method to reconstruct viral haplotypes and detect large insertions and deletions from NGS data.
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 is a R script for computing individualized genetic barrier.
InDelFixer is a java program to remove frame shift causing insertions or deletions from next-generation sequencing data.
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 performs large-scale inference on conjunctive Bayesian networks.
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 is a software package for learning and using mutagenetic trees, a family of graphical models for the accumulation of mutations.
muex is a statistical model of Mutual Exclusivity.
MutationTiming is a driver-passenger discrimination method which aims as identifying constrained cancer drivers.
NEMix is an R network inference model for learning nested effects models from single cell observations, accounting for noisy pathway activation.
netprioR is an R package for network-based integrative gene prioritisation.
OTCBN is an R package for estimating a timed conjunctive Bayesian network from paired genotype-sampling time data.
QuasiFit is a Bayesian MCMC sampler that infers fitness from a dynamic equilibrium distribution.
QuasiRecomb is a java software to infer a viral quasispecies from Next Generation Sequencing (NGS) data.
ROCR is an R package for the visualization and ROC analysis of the performance of binary classifiers.
SCITE is a C++ software package for reconstructing mutation histories of tumours based on noisy single-cell sequencing data.
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 is an R package for ranking variables according to their stability. Stability is estimated through boostrapping.
TiMEx is a Bioconductor package implementing a waiting time model for mutually exclusive cancer alterations.