{"id":167,"date":"2019-12-03T13:38:42","date_gmt":"2019-12-03T21:38:42","guid":{"rendered":"http:\/\/localhost:8888\/wordpress\/?page_id=167"},"modified":"2019-12-03T15:40:11","modified_gmt":"2019-12-03T23:40:11","slug":"resources","status":"publish","type":"page","link":"http:\/\/localhost:8888\/wordpress\/resources\/","title":{"rendered":"resources"},"content":{"rendered":"<div id=\"pl-gb167-64dc948c00160\"  class=\"panel-layout\" ><div id=\"pg-gb167-64dc948c00160-0\"  class=\"panel-grid panel-no-style\" ><div id=\"pgc-gb167-64dc948c00160-0-0\"  class=\"panel-grid-cell\" ><div id=\"panel-gb167-64dc948c00160-0-0-0\" class=\"so-panel widget widget_sow-editor panel-first-child panel-last-child\" data-index=\"0\" ><div class=\"so-widget-sow-editor so-widget-sow-editor-base\">\n<div class=\"siteorigin-widget-tinymce textwidget\">\n\t<p>Below is a compilation of resources that I often refer to for various purposes &#8211; from data visualization to sequence format conversion. With any luck, they&#8217;ll be as helpful to you as they have been to me!<\/p>\n<p>&nbsp;<\/p>\n<h3>Data visualization in R<\/h3>\n<\/div>\n<\/div><\/div><\/div><\/div><div id=\"pg-gb167-64dc948c00160-1\"  class=\"panel-grid panel-no-style\" ><div id=\"pgc-gb167-64dc948c00160-1-0\"  class=\"panel-grid-cell\" ><div id=\"panel-gb167-64dc948c00160-1-0-0\" class=\"so-panel widget widget_sow-image panel-first-child panel-last-child\" data-index=\"1\" ><div class=\"panel-widget-style panel-widget-style-for-gb167-64dc948c00160-1-0-0\" ><div class=\"so-widget-sow-image so-widget-sow-image-default-d6014b76747a\">\n\n<div class=\"sow-image-container\">\n\t<img decoding=\"async\" loading=\"lazy\" src=\"http:\/\/localhost:8888\/wordpress\/wp-content\/uploads\/2019\/12\/Color_wheel_cropped-300x290.png\" width=\"300\" height=\"290\" srcset=\"http:\/\/localhost:8888\/wordpress\/wp-content\/uploads\/2019\/12\/Color_wheel_cropped-300x290.png 300w, http:\/\/localhost:8888\/wordpress\/wp-content\/uploads\/2019\/12\/Color_wheel_cropped.png 634w\" sizes=\"(max-width: 300px) 100vw, 300px\" alt=\"\" \t\tclass=\"so-widget-image\"\/>\n<\/div>\n\n<\/div><\/div><\/div><\/div><div id=\"pgc-gb167-64dc948c00160-1-1\"  class=\"panel-grid-cell\" ><div id=\"panel-gb167-64dc948c00160-1-1-0\" class=\"so-panel widget widget_sow-editor panel-first-child panel-last-child\" data-index=\"2\" ><div class=\"panel-widget-style panel-widget-style-for-gb167-64dc948c00160-1-1-0\" ><div class=\"so-widget-sow-editor so-widget-sow-editor-base\">\n<div class=\"siteorigin-widget-tinymce textwidget\">\n\t<p>&nbsp;<\/p>\n<ul>\n<li><a href=\"http:\/\/sape.inf.usi.ch\/quick-reference\/ggplot2\/colour\">a useful references for R colors<\/a><\/li>\n<li><a href=\"https:\/\/stackoverflow.com\/questions\/15282580\/how-to-generate-a-number-of-most-distinctive-colors-in-r\">generating distinct color palettes<\/a><\/li>\n<li><a href=\"https:\/\/rstudio.com\/wp-content\/uploads\/2015\/03\/ggplot2-cheatsheet.pdf\">the ggplot2 cheat sheet<\/a> and\u00a0<a href=\"https:\/\/ggplot2.tidyverse.org\/reference\/index.html\">reference<\/a><\/li>\n<li><a href=\"http:\/\/adv-r.had.co.nz\/\">The advanced R ebook by Hadley Wickham<\/a><\/li>\n<li><a href=\"https:\/\/www.tidyverse.org\/packages\/\">Data science in R: the tidyverse<\/a><\/li>\n<\/ul>\n<\/div>\n<\/div><\/div><\/div><\/div><\/div><div id=\"pg-gb167-64dc948c00160-2\"  class=\"panel-grid panel-no-style\" ><div id=\"pgc-gb167-64dc948c00160-2-0\"  class=\"panel-grid-cell\" ><div id=\"panel-gb167-64dc948c00160-2-0-0\" class=\"so-panel widget widget_sow-editor panel-first-child panel-last-child\" data-index=\"3\" ><div class=\"so-widget-sow-editor so-widget-sow-editor-base\">\n<div class=\"siteorigin-widget-tinymce textwidget\">\n\t<h3>General sequence data manipulation<\/h3>\n<p><em><span style=\"text-decoration: underline;\">via the command line<\/span><\/em><\/p>\n<p>sam\/bam manipulation: <a href=\"https:\/\/github.com\/davetang\/learning_bam_file\">Dave Tang&#8217;s excellent repo of samtools commands<\/a><\/p>\n<p>biom manipulation:\u00a0<a href=\"http:\/\/biom-format.org\/documentation\/biom_conversion.html\"> format conversion<\/a>;\u00a0<a href=\"http:\/\/biom-format.org\/documentation\/adding_metadata.html\">metadata supplementation<\/a><\/p>\n<p>&nbsp;<\/p>\n<p><span style=\"text-decoration: underline;\"><em>via the web<\/em>\u00a0<\/span><\/p>\n<p>multiple sequence alignment (MSA) conversion: <a href=\"http:\/\/www.sing-group.org\/ALTER\/\">ALTER &#8211; a convenient web interface for MSA format conversion (especially good with phylip)<\/a><\/p>\n<p>MSA and unaligned format conversion: <a href=\"https:\/\/www.hiv.lanl.gov\/content\/sequence\/FORMAT_CONVERSION\/form.html\">Los Alamos National Lab&#8217;s sequence format converter (good for aligned or unaligned)<\/a><\/p>\n<p>&nbsp;<\/p>\n<h3>16S\/18S sequence annotation<\/h3>\n<p><a href=\"https:\/\/benjjneb.github.io\/dada2\/training.html\">default dada2-formatted reference databases<\/a><\/p>\n<p><a href=\"https:\/\/github.com\/itsmisterbrown\/updated_16S_dbs\">Silva 132 and RDP 11.5 databases (dada2 format) updated with key vaginal taxa and associated performance metrics<\/a><\/p>\n<p>&nbsp;<\/p>\n<h3>Statistics<\/h3>\n<p><a href=\"http:\/\/faculty.marshall.usc.edu\/gareth-james\/ISL\/index.html\">an excellent resource for diving into statistical learning, from the masters<\/a><\/p>\n<p><a href=\"https:\/\/stats.stackexchange.com\/questions\/30456\/geometric-interpretation-of-penalized-linear-regression\">geometric interpretation of penalization functions<\/a><\/p>\n<\/div>\n<\/div><\/div><\/div><\/div><\/div>","protected":false},"excerpt":{"rendered":"","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":6,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"_links":{"self":[{"href":"http:\/\/localhost:8888\/wordpress\/wp-json\/wp\/v2\/pages\/167"}],"collection":[{"href":"http:\/\/localhost:8888\/wordpress\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"http:\/\/localhost:8888\/wordpress\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"http:\/\/localhost:8888\/wordpress\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/localhost:8888\/wordpress\/wp-json\/wp\/v2\/comments?post=167"}],"version-history":[{"count":4,"href":"http:\/\/localhost:8888\/wordpress\/wp-json\/wp\/v2\/pages\/167\/revisions"}],"predecessor-version":[{"id":175,"href":"http:\/\/localhost:8888\/wordpress\/wp-json\/wp\/v2\/pages\/167\/revisions\/175"}],"wp:attachment":[{"href":"http:\/\/localhost:8888\/wordpress\/wp-json\/wp\/v2\/media?parent=167"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}