Format

Send to

Choose Destination
Bioinformatics. 2016 Aug 1;32(15):2359-60. doi: 10.1093/bioinformatics/btw127. Epub 2016 Mar 26.

SNPhood: investigate, quantify and visualise the epigenomic neighbourhood of SNPs using NGS data.

Author information

1
European Molecular Biology Laboratory (EMBL), Heidelberg, 69117, Germany.

Abstract

MOTIVATION:

The vast majority of the many thousands of disease-associated single nucleotide polymorphisms (SNPs) lie in the non-coding part of the genome. They are likely to affect regulatory elements, such as enhancers and promoters, rather than the function of a protein. To understand the molecular mechanisms underlying genetic diseases, it is therefore increasingly important to study the effect of a SNP on nearby molecular traits such as chromatin or transcription factor binding.

RESULTS:

We developed SNPhood, a user-friendly Bioconductor R package to investigate, quantify and visualise the local epigenetic neighbourhood of a set of SNPs in terms of chromatin marks or TF binding sites using data from NGS experiments.

AVAILABILITY AND IMPLEMENTATION:

SNPhood is publicly available and maintained as an R Bioconductor package at http://bioconductor.org/packages/SNPhood/

CONTACT:

judith.zaugg@embl.de

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
27153574
PMCID:
PMC4965630
DOI:
10.1093/bioinformatics/btw127
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Silverchair Information Systems Icon for PubMed Central
Loading ...
Support Center