BIMr (Bayesian Inference of imMigration rates) is a free software that makes inferences about recent proportions of immigrant genes in subdivided populations and that identifies the environmental factors that are responsible for observed gene flow patterns.
clonealign assigns single-cell RNA-seq expression to cancer clones by probabilistically mapping RNA-seq to clone-specific copy number profiles using reparametrization gradient variational inference.
biRte is an software for bayesian prediction of TF and miRNA activities from different expression data entities; interfaces nem for gene regulatory network inference.
BitSeq is an application for inferring expression levels of individual transcripts from sequencing (RNA-Seq) data and estimating differential expression (DE) between conditions. An advantage of this approach is the ability to account for both technical uncertainty and intrinsic biological variance in order to avoid false DE calls. The technical contribution to the uncertainty comes both from finite read-depth and the possibly ambiguous mapping of reads to multiple transcripts.
BIRTA uses the regulatory networks of TFs and miRNAs together with mRNA and miRNA expression data to predict switches in regulatory activity between two conditions. A Bayesian network is used to model the regulatory structure and Markov-Chain-Monte-Carlo is applied to sample the activity states.
::DEVELOPER
Benedikt Zacher <zacher at lmb.uni-muenchen.de>, Holger Froehlich <frohlich at bit.uni-bonn.de>
BayesAss is a software that uses individual multilocus genotypes to estimate rates of recent immigration (over the last several generations) among populations is presented. The software also estimates the posterior probability distributions of individual immigrant ancestries, population allele frequencies, population inbreeding coefficients, and other parameters of potential interest.
PhyBayes is a program for Bayesian inference in phylogenetics
– estimation of divergence dates / rates of molecular evolution
– Bayes factor and test of evolutionary hypotheses
– tree space search and estimation of the posterior probabilities
– estimation of heterogeneities in a data set (still a project…)