Finding regions showing high expression ab initio using bumphunter
The bumphunter package in R’s Bioconductor ecosystem is a tool for identifying genomic regions that exhibit bumps of enrichment in high-throughput sequencing data. These bumps may represent functional regions, such as enhancers or transcription factor binding sites, and the package can be used to identify both known and novel regions of interest.
The bumphunter package works by scanning a given genomic region to enrich a particular feature of interest, such as the presence of certain transcription factor binding sites, or the level of histone modifications. It does this by dividing the region into non-overlapping windows and comparing the mean signal within each window to the overall mean signal across the entire region. The package then employs a statistical model to determine whether any particular window is significantly enriched for the feature of interest.
bumphunter can be used to identify novel enhancer...
