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title: 'SNPhood: SNPhood: Investigate, quantify and visualise the epigenomic neighbourhood
  of SNPs using NGS data'
version: 1.35.0
abstract: To date, thousands of single nucleotide polymorphisms (SNPs) have been found
  to be associated with complex traits and diseases. However, the vast majority of
  these disease-associated SNPs lie in the non-coding part of the genome, and are
  likely to affect regulatory elements, such as enhancers and promoters, rather than
  function of a protein. Thus, to understand the molecular mechanisms underlying genetic
  traits and diseases, it becomes increasingly important to study the effect of a
  SNP on nearby molecular traits such as chromatin environment or transcription factor
  (TF) binding. Towards this aim, we developed SNPhood, a user-friendly *Bioconductor*
  R package to investigate and visualize the local neighborhood of a set of SNPs of
  interest for NGS data such as chromatin marks or transcription factor binding sites
  from ChIP-Seq or RNA- Seq experiments. SNPhood comprises a set of easy-to-use functions
  to extract, normalize and summarize reads for a genomic region, perform various
  data quality checks, normalize read counts using additional input files, and to
  cluster and visualize the regions according to the binding pattern. The regions
  around each SNP can be binned in a user-defined fashion to allow for analysis of
  very broad patterns as well as a detailed investigation of specific binding shapes.
  Furthermore, SNPhood supports the integration with genotype information to investigate
  and visualize genotype-specific binding patterns. Finally, SNPhood can be employed
  for determining, investigating, and visualizing allele-specific binding patterns
  around the SNPs of interest.
authors:
- family-names: Arnold
  given-names: Christian
  email: christian.arnold@embl.de
- family-names: Bhat
  given-names: Pooja
  email: pooja.bhat@embl.de
- family-names: Zaugg
  given-names: Judith
  email: judith.zaugg@embl.de
repository: https://bioc.r-universe.dev
url: https://bioconductor.org/packages/SNPhood
contact:
- family-names: Arnold
  given-names: Christian
  email: christian.arnold@embl.de