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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.

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).