{"id":260,"date":"2017-05-05T14:55:02","date_gmt":"2017-05-05T14:55:02","guid":{"rendered":"https:\/\/wordpress.clarku.edu\/jdresch\/?page_id=260"},"modified":"2017-10-10T15:14:40","modified_gmt":"2017-10-10T15:14:40","slug":"software","status":"publish","type":"page","link":"https:\/\/wordpress.clarku.edu\/jdresch\/?page_id=260","title":{"rendered":"Software"},"content":{"rendered":"<p>Folded&nbsp;<em>k<\/em>-spectrum kernel:&nbsp;<a href=\"https:\/\/github.com\/elmasee\/folks\">https:\/\/github.com\/elmasee\/folks<\/a><br \/>\n(Reference: Elmas A, Wang X, Dresch JM (2017) The folded <em>k<\/em>-spectrum kernel: A machine learning approach to detecting transcription factor binding sites with gapped nucleotide dependencies. <em>PLoS ONE<\/em> 12(10): e0185570.)<\/p>\n<p>Thermodynamic-based Model:&nbsp;<a href=\"https:\/\/github.com\/arnosti-lab\">https:\/\/github.com\/arnosti-lab<br \/>\n<\/a>(Reference:&nbsp;*Sayal R, *Dresch JM,&nbsp;Pushel I,&nbsp;Taylor BR, Arnosti DN&nbsp;(2016)&nbsp;Quantitative perturbation-based analysis of gene expression in early&nbsp;<em>Drosophila<\/em>&nbsp;embryo.&nbsp;<em>eLife&nbsp;<\/em>5:e08445 (* \u2013 equal contribution))<\/p>\n<p>MARZ algorithm:&nbsp;<a href=\"https:\/\/wordpress.clarku.edu\/wp-content\/uploads\/sites\/383\/2017\/05\/marzscaled.zip\">marzscaled<br \/>\n<\/a>(Reference: Zellers RG, Drewell RA, Dresch JM (2015)&nbsp;MARZ: An algorithm to combinatorially analyze gapped&nbsp;<em>n<\/em>-mer models of transcription factor binding.&nbsp;<em>BMC Bioinformatics.&nbsp;<\/em>16: 30.)<a href=\"https:\/\/wordpress.clarku.edu\/wp-content\/uploads\/sites\/383\/2017\/05\/marzscaled.zip\"><br \/>\n<\/a><\/p>\n<p>&nbsp;<\/p>\n<p>Any questions regarding software should be directed to Jacqueline Dresch at jdresch@clarku.edu.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Folded&nbsp;k-spectrum kernel:&nbsp;https:\/\/github.com\/elmasee\/folks (Reference: Elmas A, Wang X, Dresch JM (2017) The folded k-spectrum kernel: A machine learning approach to detecting transcription factor binding sites with gapped nucleotide dependencies. PLoS ONE 12(10): e0185570.) Thermodynamic-based Model:&nbsp;https:\/\/github.com\/arnosti-lab (Reference:&nbsp;*Sayal R, *Dresch JM,&nbsp;Pushel I,&nbsp;Taylor BR, &hellip; <a href=\"https:\/\/wordpress.clarku.edu\/jdresch\/?page_id=260\">Continue reading <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":571,"featured_media":0,"parent":0,"menu_order":5,"comment_status":"closed","ping_status":"closed","template":"","meta":{"ngg_post_thumbnail":0,"footnotes":""},"class_list":["post-260","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/wordpress.clarku.edu\/jdresch\/index.php?rest_route=\/wp\/v2\/pages\/260","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/wordpress.clarku.edu\/jdresch\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/wordpress.clarku.edu\/jdresch\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/wordpress.clarku.edu\/jdresch\/index.php?rest_route=\/wp\/v2\/users\/571"}],"replies":[{"embeddable":true,"href":"https:\/\/wordpress.clarku.edu\/jdresch\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=260"}],"version-history":[{"count":0,"href":"https:\/\/wordpress.clarku.edu\/jdresch\/index.php?rest_route=\/wp\/v2\/pages\/260\/revisions"}],"wp:attachment":[{"href":"https:\/\/wordpress.clarku.edu\/jdresch\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=260"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}