We tested whether self-organizing maps (SOMs) could be used to effectively integrate,
visualize, and mine diverse genomics data types, including complex chromatin signatures. A …

CHROMATRA (CHROmatin Mapping Across TRAnscripts) is a visualization tool available as
plug-in for the Galaxy platform. It allows detailed yet concise presentations of data derived …

Abstract ChIP-Atlas (https://chip-atlas. org/) presents a suite of data-mining tools for
analyzing epigenomic landscapes, powered by the comprehensive integration of over 376 …

Current genome-wide ChIP-seq experiments on different epigenetic marks aim at unraveling
the interplay between their regulation mechanisms. Published evaluation tools, however …

Gene regulation at functional elements (eg, enhancers, promoters, insulators) is governed
by an interplay of nucleosome remodeling, histone modifications, and transcription factor …

Chromatin modifications orchestrate the dynamic regulation of gene expression during
development and in disease. Bulk approaches have characterized the wide repertoire of …

Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is an increasingly
common experimental approach to generate genome-wide maps of histone modifications …

Rapid advances in single-cell assays have outpaced methods for analysis of those data
types. Different single-cell assays show extensive variation in sensitivity and signal to noise …

Non-coding regulatory elements such as enhancers are key in controlling the cell-type
specificity and spatio-temporal expression of genes. To drive stable and precise gene …

Methods for cell clustering and gene expression from single-cell RNA sequencing (scRNA-
seq) data are essential for biological interpretation of cell processes. Here, we present …