{"id":854,"date":"2022-06-02T15:50:46","date_gmt":"2022-06-02T15:50:46","guid":{"rendered":"https:\/\/www.embl.org\/groups\/zaugg\/?page_id=854"},"modified":"2022-06-07T09:27:56","modified_gmt":"2022-06-07T09:27:56","slug":"resources-snphood-investigate-quantify-and-visualise-the-epigenomic-neighbourhood-of-snps-using-ngs-data-bioinformatics-2016","status":"publish","type":"page","link":"https:\/\/www.embl.org\/groups\/zaugg\/data-and-tools\/resources-snphood-investigate-quantify-and-visualise-the-epigenomic-neighbourhood-of-snps-using-ngs-data-bioinformatics-2016\/","title":{"rendered":"Resources: SNPhood: investigate, quantify and visualise the epigenomic neighbourhood of SNPs using NGS data (Bioinformatics 2016)"},"content":{"rendered":"\n<p id=\"p-2\">Motivation:&nbsp;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.<\/p>\n\n\n\n<p id=\"p-3\">Results:&nbsp;We developed&nbsp;<em>SNPhood<\/em>, a user-friendly&nbsp;<em>Bioconductor<\/em>&nbsp;R package to investigate, quantify and visualize the local epigenetic neighbourhood of a set of SNPs in terms of chromatin marks or TF binding sites using data from NGS experiments.<\/p>\n\n\n\n<p id=\"p-4\">Availability:&nbsp;SNPhood is publicly available and maintained as an R Bioconductor package at&nbsp;<a href=\"http:\/\/bioconductor.org\/packages\/SNPhood\/\">http:\/\/bioconductor.org\/packages\/SNPhood\/<\/a>.<\/p>\n\n\n\n<div class=\"wp-block-image\"><figure class=\"vf-figure  | vf-figure--align vf-figure--align-centered  size-large\"><img loading=\"lazy\" decoding=\"async\" width=\"620\" height=\"915\" class=\"vf-figure__image\" src=\"https:\/\/www.embl.org\/groups\/zaugg\/wp-content\/uploads\/2022\/06\/Figure1-2-620x915-1.png\" alt=\"\" class=\"wp-image-1068\" srcset=\"https:\/\/www.embl.org\/groups\/zaugg\/wp-content\/uploads\/2022\/06\/Figure1-2-620x915-1.png 620w, https:\/\/www.embl.org\/groups\/zaugg\/wp-content\/uploads\/2022\/06\/Figure1-2-620x915-1-203x300.png 203w\" sizes=\"auto, (max-width: 620px) 100vw, 620px\" \/><\/figure><\/div>\n","protected":false},"excerpt":{"rendered":"<p>Motivation:&nbsp;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&hellip;<\/p>\n","protected":false},"author":10,"featured_media":0,"parent":816,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"footnotes":""},"embl_taxonomy":[],"class_list":["post-854","page","type-page","status-publish","hentry"],"acf":[],"embl_taxonomy_terms":[],"_links":{"self":[{"href":"https:\/\/www.embl.org\/groups\/zaugg\/wp-json\/wp\/v2\/pages\/854","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.embl.org\/groups\/zaugg\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.embl.org\/groups\/zaugg\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.embl.org\/groups\/zaugg\/wp-json\/wp\/v2\/users\/10"}],"replies":[{"embeddable":true,"href":"https:\/\/www.embl.org\/groups\/zaugg\/wp-json\/wp\/v2\/comments?post=854"}],"version-history":[{"count":2,"href":"https:\/\/www.embl.org\/groups\/zaugg\/wp-json\/wp\/v2\/pages\/854\/revisions"}],"predecessor-version":[{"id":1076,"href":"https:\/\/www.embl.org\/groups\/zaugg\/wp-json\/wp\/v2\/pages\/854\/revisions\/1076"}],"up":[{"embeddable":true,"href":"https:\/\/www.embl.org\/groups\/zaugg\/wp-json\/wp\/v2\/pages\/816"}],"wp:attachment":[{"href":"https:\/\/www.embl.org\/groups\/zaugg\/wp-json\/wp\/v2\/media?parent=854"}],"wp:term":[{"taxonomy":"embl_taxonomy","embeddable":true,"href":"https:\/\/www.embl.org\/groups\/zaugg\/wp-json\/wp\/v2\/embl_taxonomy?post=854"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}