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Chromatin-state identification software tools | DNA-protein interaction data analysis

Readout of genetic information in eukaryotic genomes is mediated by the dynamic chromatin environment, which regulates DNA accessibility for the gene expression machinery through chromatin compaction, associated histone modifications and incorporation of histone variants. Source text: Sohn et al., 2015.

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CMINT / Chromatin Module INference on Trees
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Identifies chromatin modules in multiple cell types simultaneously. CMINT is a generative probabilistic graphical model-based approach for multitask clustering. It was developed to enable systematic characterization of chromatin state dynamics across multiple related cell types. CMINT is motivated by the hierarchical structure of developmental lineages, where a new cell type arises from a predecessor through several intermediate states.
OrbWeaver
Allow users to predict cell type-specific effects of single nucleotide polymorphism (SNPs) on chromatin activity. OrbWeaver can identify trans-acting elements driving cellular differences in chromatin accessibility and can determine effects of genetic variation in a cell type-specific manner. Moreover, it assists users to detect transcription factors (TFs) with known cell type-specific effects and can ascertain direction of effect of the cell type-specific chromatin accessibility quantitative trait locis (caQTLs).
StatePaintR
Facilitates the use of StateHub models to generate browser tracks for bioinformatic analyses. StatePaintR is a software package which translates epigenomics files into segmentations using these models. It calculates quantitative state scores based on genome-wide ranking, allowing prioritization and enrichment testing and facilitating quantitative analysis. The software can be used as part of a workflow with uniformly processed data to generate reproducible annotations from public and private data.
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