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Showing 3 records out of 3 total
CT-CBN [Computational Biology (N. Beerenwinkel)]
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Categories: phylogeny/evolution, population genetics - Software type(s): CLI - tool
Continuous time conjunctive Bayesian networks (ct-cbn) are a family of graphical models describing the accumulation of mutations under order constraints. The software allows for the estimation of the network from cross-sectional data, such as mutation profiles of cancer or HIV patients.
keywords: Bayesian network, conjunctive Bayesian network, genetic progression, graphical model, partial order
MARA [Genome Systems Biology (E. van Nimwegen)]
UP
Categories: genomics, (characterisation/annotation), systems biology, transcriptomics - Software type(s): website, GUI - tool
MARA models genome-wide expression data in terms of our genome-wide annotations of regulatory sites. For a given expression data-set it infers the key transcription regulators, their sample-dependent activities, and their genome-wide targets.
keywords: Affymetrix chip analysis, animal, arthropod, Bayesian network, ChIP-seq, eukaryotic promoter, expression, expression data, fungi, genetic data analysis, genomics, graphics, HMM, human, insect, in situ hybridization, interaction, maximum likelihood, microarray, network, NGS, regulatory site, sequence analysis, sequencing, transcription factor binding site, transcription module, transcription regulation, transcription start site annotation, transcriptome analysis, vertebrate
Phylogibbs [Genome Systems Biology (E. van Nimwegen)]
UP
Categories: genomics, (sequence alignment, similarity search), systems biology - Software type(s): website, CLI, GUI - tool
Phylogibbs is an algorithm for discovering regulatory sites in a collection of DNA sequences, including multiple alignments of orthologous sequences from related organisms.The algorithm uses a Gibbs sampling strategy, takes the phylogenetic relationships of the input sequences rigorously into account, and assigns realistic posterior probabilities to reported sites using a novel annealing+tracking strategy.
keywords: alignment, alignment analysis, animal, arthropod, Bayesian network, binding sites prediction, C, ChIP-seq, evolution, fungi, genetic data analysis, genomics, Gibbs sampler, HMM, human, insect, interaction, maximum likelihood, model of evolution, multiple sequence alignment (MSA), network, NGS, phylogibbs, population genetics, regulatory site, selection, sequence analysis, sequence comparison, short sequence alignment, similarity search, transcription factor binding site, transcription module, transcription regulation, transcriptome analysis, vertebrate