{"id":224,"date":"2023-09-12T11:14:56","date_gmt":"2023-09-12T08:14:56","guid":{"rendered":"https:\/\/sites.uef.fi\/bioinformatics\/?page_id=224"},"modified":"2026-01-26T17:14:21","modified_gmt":"2026-01-26T15:14:21","slug":"services","status":"publish","type":"page","link":"https:\/\/sites.uef.fi\/bioinformatics\/services\/","title":{"rendered":"Analysis Services"},"content":{"rendered":"\n<p>The UEF Bioinformatics Center provides computing, data analysis, and consultancy services. The Bioinformatics Center has expertise especially in processing data from different omics technologies. Our services include, for example, experimental design, data analysis and visualization, and workflow development (see below).<\/p>\n\n\n\n<p>The Bioinformatics Center offers services for the UEF research community but the services are equally available to other Finnish research institutions and non-academic customers. The project requests are evaluated together with the customer based on expertise, feasibility and available resources. Computing services are available only to the UEF health sciences researchers and students.<\/p>\n\n\n\n<p>Reports describing the analysis tools and methods used, along with the analysis results, are provided at the end of each project. The data are analyzed using widely used, freely available tools and published or in-house developed workflows. <\/p>\n\n\n\n<p>The computing services and short consultancy services are provided free of charge, but the data analysis and longer consultancy services are charged based on project fees and actual working hours. More information on the pricing can be found <a href=\"https:\/\/sites.uef.fi\/bioinformatics\/pricing\/\">here<\/a>.<\/p>\n\n\n\n<p>For the use of our services, we request that you acknowledge our contribution with either an acknowledgment or authorship in each scientific article. See more detailed information regarding authorship and acknowledging <a href=\"https:\/\/sites.uef.fi\/bioinformatics\/acknowledge\/\">here<\/a>.<\/p>\n\n\n\n<figure class=\"wp-block-image aligncenter size-large is-resized\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"972\" src=\"https:\/\/sites.uef.fi\/bioinformatics\/wp-content\/uploads\/sites\/425\/2025\/03\/bic_v2-1024x972.png\" alt=\"\" class=\"wp-image-1159\" style=\"width:538px;height:auto\" srcset=\"https:\/\/sites.uef.fi\/bioinformatics\/wp-content\/uploads\/sites\/425\/2025\/03\/bic_v2-1024x972.png 1024w, https:\/\/sites.uef.fi\/bioinformatics\/wp-content\/uploads\/sites\/425\/2025\/03\/bic_v2-300x285.png 300w, https:\/\/sites.uef.fi\/bioinformatics\/wp-content\/uploads\/sites\/425\/2025\/03\/bic_v2-768x729.png 768w, https:\/\/sites.uef.fi\/bioinformatics\/wp-content\/uploads\/sites\/425\/2025\/03\/bic_v2-1536x1458.png 1536w, https:\/\/sites.uef.fi\/bioinformatics\/wp-content\/uploads\/sites\/425\/2025\/03\/bic_v2.png 1636w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><\/figure>\n\n\n\n<p>Here you can find detailed descriptions of our services. If the service you are interested in is not listed below, we encourage you to <a href=\"https:\/\/sites.uef.fi\/bioinformatics\/contact-information\/\">contact us<\/a> for further assistance!<\/p>\n\n\n\t<div id=\"accordion-block_4f0243b4c76575c5f9c276e3c9117fa7\" class=\"accordions\">\n\t\t\t\t\t<div class=\"accordion accordion-js\">\n\t\t\t\t<button class=\"accordion__button\" aria-controls=\"content-9963\" aria-expanded=\"false\" id=\"accordion-control-9963\">\n\t\t\t\t\t<h3 class=\"accordion__heading\" >\n\t\t\t\t\t\tGenomics\t\t\t\t\t<\/h3>\n\t\t\t\t<\/button>\n\t\t\t\t<div class=\"accordion__content\" role=\"region\" aria-labelledby=\"accordion-control-9963\" aria-hidden=\"true\" id=\"content-9963\">\n\t\t\t\t\t<p>Our genomics services include:<\/p>\n<ul>\n<li><strong>GWAS: genome-wide association analysis<\/strong>\n<ul>\n<li>\n<div>Conducted using an in-house pipeline for genomic data quality control and association analyses with Plink2<\/div>\n<\/li>\n<li>\n<div>GWAS are available for case-control and continuous phenotypes<\/div>\n<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<ul>\n<li><strong>Genomic imputation<\/strong>\n<ul>\n<li>Quality control and filtering performed using an in-house pipeline<\/li>\n<li>Performed using the Finnish Institute for Health and Welfare (THL) Biobank\u2019s <a href=\"https:\/\/finngen.gitbook.io\/documentation\/methods\/genotype-imputation\/sisu-reference-panel\">SISu<\/a> reference panel (v.4.2 or v.3)<\/li>\n<li>More information can be found <a href=\"https:\/\/sites.uef.fi\/bioinformatics\/genomic-imputation-service\/\">here<\/a><\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<ul>\n<li><strong>Variant calling<\/strong>\n<ul>\n<li>Preprocessing and variant calling is executed using the <a style=\"font-size: 1rem\" href=\"https:\/\/nf-co.re\/sarek\/3.5.1\/\">nf-core\/sarek<\/a><span style=\"font-size: 1rem\"> pipeline and\/or<\/span><\/li>\n<li><a style=\"font-size: 1rem\" href=\"https:\/\/github.com\/broadinstitute\/gatk\">GATK<\/a>\/<span data-teams=\"true\">HaplotypeCaller<\/span><span style=\"font-size: 1rem\">\u00a0<span data-teams=\"true\">or <a href=\"https:\/\/github.com\/google\/deepvariant\">Deepvariant<\/a> methods used for germline and <\/span><\/span>GATK\/Mutect2 for somatic variant calling<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<ul>\n<li><strong>PheWeb<\/strong>\n<ul>\n<li>A customized version of <a href=\"https:\/\/github.com\/statgen\/pheweb\">PheWeb<\/a> for exploring your GWAS results<\/li>\n<li>New functionality for comparing your GWAS against <a href=\"https:\/\/www.finngen.fi\/en\">FinnGen<\/a> results<\/li>\n<li>Standard PheWeb features such as PheWAS and reference results from <a href=\"https:\/\/www.ukbiobank.ac.uk\/about-our-data\/\">UK Biobank<\/a> and the <a href=\"https:\/\/www.ebi.ac.uk\/gwas\/\">GWAS Catalog<\/a><\/li>\n<li>Instances can be built to meet customer-specific requirements<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n\t\t\t\t<\/div>\n\t\t\t<\/div>\n\t\t\t\t\t<div class=\"accordion accordion-js\">\n\t\t\t\t<button class=\"accordion__button\" aria-controls=\"content-6341\" aria-expanded=\"false\" id=\"accordion-control-6341\">\n\t\t\t\t\t<h3 class=\"accordion__heading\" >\n\t\t\t\t\t\tEpigenomics\t\t\t\t\t<\/h3>\n\t\t\t\t<\/button>\n\t\t\t\t<div class=\"accordion__content\" role=\"region\" aria-labelledby=\"accordion-control-6341\" aria-hidden=\"true\" id=\"content-6341\">\n\t\t\t\t\t<p>Our epigenomics services include:<\/p>\n<ul>\n<li><strong>ATAC-seq: transposase-accessible chromatin sequencing<\/strong>\n<ul>\n<li>Data quality control is conducted using the <a href=\"https:\/\/nf-co.re\/atacseq\/2.1.2\/\">nf-core\/atacseq<\/a> pipeline<\/li>\n<li>Differential accessibility, peak calling, functional enrichment\/ pathway analyses and visualization are conducted using an in-house pipeline based on the <a href=\"https:\/\/github.com\/reskejak\/ATAC-seq\">methodology<\/a> developed by <a href=\"https:\/\/epigeneticsandchromatin.biomedcentral.com\/articles\/10.1186\/s13072-020-00342-y\">Reske et al<\/a>.<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<ul>\n<li><strong>ChIP-seq: chromatin immunoprecipitation sequencing<\/strong>\n<ul>\n<li>\n<div>Data quality control and analysis is conducted using the <a href=\"https:\/\/nf-co.re\/chipseq\/2.1.0\">nf-core\/chipseq<\/a> pipeline<\/div>\n<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n\t\t\t\t<\/div>\n\t\t\t<\/div>\n\t\t\t\t\t<div class=\"accordion accordion-js\">\n\t\t\t\t<button class=\"accordion__button\" aria-controls=\"content-7484\" aria-expanded=\"false\" id=\"accordion-control-7484\">\n\t\t\t\t\t<h3 class=\"accordion__heading\" >\n\t\t\t\t\t\tTranscriptomics\t\t\t\t\t<\/h3>\n\t\t\t\t<\/button>\n\t\t\t\t<div class=\"accordion__content\" role=\"region\" aria-labelledby=\"accordion-control-7484\" aria-hidden=\"true\" id=\"content-7484\">\n\t\t\t\t\t<p>Our transcriptomics services include:<\/p>\n<ul>\n<li><strong>RNA-seq: bulk RNA-sequencing<\/strong>\n<ul>\n<li>\n<div>Measures gene expression across entire samples<\/div>\n<\/li>\n<li>Data preprocessing and quality control is conducted using the <a href=\"https:\/\/nf-co.re\/rnaseq\/3.18.0\">nf-core\/rnaseq<\/a> pipeline<\/li>\n<li>Differential expression, functional enrichment\/ pathway analyses and visualization are conducted using an in-house pipeline<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<ul>\n<li>\n<div><strong>scRNA-seq (Single-Cell RNA-Sequencing)<\/strong><\/div>\n<ul>\n<li>\n<div>Measures gene expression at the single-cell level<\/div>\n<\/li>\n<li>Single-cell data generated with 10X Genomics technologies is preprocessed using <a href=\"https:\/\/www.10xgenomics.com\/support\/software\/cell-ranger\/latest\">Cell Ranger<\/a><\/li>\n<li>Basic analysis includes data filtering, dimensional reduction, clustering, differential expression, trajectory, functional enrichment\/pathway analyses and visualization<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n\t\t\t\t<\/div>\n\t\t\t<\/div>\n\t\t\t\t\t<div class=\"accordion accordion-js\">\n\t\t\t\t<button class=\"accordion__button\" aria-controls=\"content-1740\" aria-expanded=\"false\" id=\"accordion-control-1740\">\n\t\t\t\t\t<h3 class=\"accordion__heading\" >\n\t\t\t\t\t\tCustomized services and consulting\t\t\t\t\t<\/h3>\n\t\t\t\t<\/button>\n\t\t\t\t<div class=\"accordion__content\" role=\"region\" aria-labelledby=\"accordion-control-1740\" aria-hidden=\"true\" id=\"content-1740\">\n\t\t\t\t\t<p><span style=\"font-size: 1rem\">We provide tailored analysis and consulting services, including but not limited to:<\/span><\/p>\n<div>\n<ul>\n<li><strong>Multiomics\/Multimodal Data Analyses<\/strong>\n<ul>\n<li>Integrating diverse datasets (e.g., genomics, transcriptomics, proteomics, metabolomics, clinical variables) for comprehensive insights<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<ul>\n<li><strong>Metabolomics<\/strong>\n<ul>\n<li>Multivariate analysis of metabolic profiles<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<ul>\n<li><strong>Proteomics <\/strong>\n<ul>\n<li>Processing and analysis of e.g. Olink data<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<ul>\n<li><strong>Customised <\/strong><strong>Statistical<\/strong><strong> and Machine Learning<\/strong><strong> Analyses<\/strong>\n<ul>\n<li>Applying\/consulting on proper statistical methods<\/li>\n<li>Help in designing experiments to maximize research impact<\/li>\n<li>Longitudinal modeling<\/li>\n<li>Survival analyses for modeling time-to-event data<\/li>\n<li>Developing predictive models and automated workflows<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<ul>\n<li><strong>Data Visualization Service<\/strong>\n<ul>\n<li>Creating publication-ready visualization<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<\/div>\n\t\t\t\t<\/div>\n\t\t\t<\/div>\n\t\t\t<\/div>\n\t","protected":false},"excerpt":{"rendered":"<p>The UEF Bioinformatics Center provides computing, data analysis, and consultancy services. The Bioinformatics Center has expertise especially in processing data from different omics technologies. Our services include, for example, experimental design, data analysis and visualization, and workflow development (see below). The Bioinformatics Center offers services for the UEF research community but the services are equally [&hellip;]<\/p>\n","protected":false},"author":990,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"footnotes":""},"class_list":["post-224","page","type-page","status-publish","hentry"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.1.1 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Analysis Services - UEF Bioinformatics Center<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/sites.uef.fi\/bioinformatics\/services\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Analysis Services - UEF Bioinformatics Center\" \/>\n<meta property=\"og:description\" content=\"The UEF Bioinformatics Center provides computing, data analysis, and consultancy services. The Bioinformatics Center has expertise especially in processing data from different omics technologies. Our services include, for example, experimental design, data analysis and visualization, and workflow development (see below). The Bioinformatics Center offers services for the UEF research community but the services are equally [&hellip;]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/sites.uef.fi\/bioinformatics\/services\/\" \/>\n<meta property=\"og:site_name\" content=\"UEF Bioinformatics Center\" \/>\n<meta property=\"article:modified_time\" content=\"2026-01-26T15:14:21+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/sites.uef.fi\/bioinformatics\/wp-content\/uploads\/sites\/425\/2025\/03\/bic_v2.png\" \/>\n\t<meta property=\"og:image:width\" content=\"1636\" \/>\n\t<meta property=\"og:image:height\" content=\"1553\" \/>\n\t<meta property=\"og:image:type\" content=\"image\/png\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:label1\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data1\" content=\"2 minutes\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"WebPage\",\"@id\":\"https:\/\/sites.uef.fi\/bioinformatics\/services\/\",\"url\":\"https:\/\/sites.uef.fi\/bioinformatics\/services\/\",\"name\":\"Analysis Services - UEF Bioinformatics Center\",\"isPartOf\":{\"@id\":\"https:\/\/sites.uef.fi\/bioinformatics\/#website\"},\"primaryImageOfPage\":{\"@id\":\"https:\/\/sites.uef.fi\/bioinformatics\/services\/#primaryimage\"},\"image\":{\"@id\":\"https:\/\/sites.uef.fi\/bioinformatics\/services\/#primaryimage\"},\"thumbnailUrl\":\"https:\/\/sites.uef.fi\/bioinformatics\/wp-content\/uploads\/sites\/425\/2025\/03\/bic_v2-1024x972.png\",\"datePublished\":\"2023-09-12T08:14:56+00:00\",\"dateModified\":\"2026-01-26T15:14:21+00:00\",\"breadcrumb\":{\"@id\":\"https:\/\/sites.uef.fi\/bioinformatics\/services\/#breadcrumb\"},\"inLanguage\":\"en-US\",\"potentialAction\":[{\"@type\":\"ReadAction\",\"target\":[\"https:\/\/sites.uef.fi\/bioinformatics\/services\/\"]}]},{\"@type\":\"ImageObject\",\"inLanguage\":\"en-US\",\"@id\":\"https:\/\/sites.uef.fi\/bioinformatics\/services\/#primaryimage\",\"url\":\"https:\/\/sites.uef.fi\/bioinformatics\/wp-content\/uploads\/sites\/425\/2025\/03\/bic_v2.png\",\"contentUrl\":\"https:\/\/sites.uef.fi\/bioinformatics\/wp-content\/uploads\/sites\/425\/2025\/03\/bic_v2.png\",\"width\":1636,\"height\":1553},{\"@type\":\"BreadcrumbList\",\"@id\":\"https:\/\/sites.uef.fi\/bioinformatics\/services\/#breadcrumb\",\"itemListElement\":[{\"@type\":\"ListItem\",\"position\":1,\"name\":\"Home\",\"item\":\"https:\/\/sites.uef.fi\/bioinformatics\/\"},{\"@type\":\"ListItem\",\"position\":2,\"name\":\"Analysis Services\"}]},{\"@type\":\"WebSite\",\"@id\":\"https:\/\/sites.uef.fi\/bioinformatics\/#website\",\"url\":\"https:\/\/sites.uef.fi\/bioinformatics\/\",\"name\":\"UEF Bioinformatics Center\",\"description\":\"\",\"potentialAction\":[{\"@type\":\"SearchAction\",\"target\":{\"@type\":\"EntryPoint\",\"urlTemplate\":\"https:\/\/sites.uef.fi\/bioinformatics\/?s={search_term_string}\"},\"query-input\":{\"@type\":\"PropertyValueSpecification\",\"valueRequired\":true,\"valueName\":\"search_term_string\"}}],\"inLanguage\":\"en-US\"}]}<\/script>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"Analysis Services - UEF Bioinformatics Center","robots":{"index":"index","follow":"follow","max-snippet":"max-snippet:-1","max-image-preview":"max-image-preview:large","max-video-preview":"max-video-preview:-1"},"canonical":"https:\/\/sites.uef.fi\/bioinformatics\/services\/","og_locale":"en_US","og_type":"article","og_title":"Analysis Services - UEF Bioinformatics Center","og_description":"The UEF Bioinformatics Center provides computing, data analysis, and consultancy services. The Bioinformatics Center has expertise especially in processing data from different omics technologies. Our services include, for example, experimental design, data analysis and visualization, and workflow development (see below). The Bioinformatics Center offers services for the UEF research community but the services are equally [&hellip;]","og_url":"https:\/\/sites.uef.fi\/bioinformatics\/services\/","og_site_name":"UEF Bioinformatics Center","article_modified_time":"2026-01-26T15:14:21+00:00","og_image":[{"width":1636,"height":1553,"url":"https:\/\/sites.uef.fi\/bioinformatics\/wp-content\/uploads\/sites\/425\/2025\/03\/bic_v2.png","type":"image\/png"}],"twitter_card":"summary_large_image","twitter_misc":{"Est. reading time":"2 minutes"},"schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"WebPage","@id":"https:\/\/sites.uef.fi\/bioinformatics\/services\/","url":"https:\/\/sites.uef.fi\/bioinformatics\/services\/","name":"Analysis Services - UEF Bioinformatics Center","isPartOf":{"@id":"https:\/\/sites.uef.fi\/bioinformatics\/#website"},"primaryImageOfPage":{"@id":"https:\/\/sites.uef.fi\/bioinformatics\/services\/#primaryimage"},"image":{"@id":"https:\/\/sites.uef.fi\/bioinformatics\/services\/#primaryimage"},"thumbnailUrl":"https:\/\/sites.uef.fi\/bioinformatics\/wp-content\/uploads\/sites\/425\/2025\/03\/bic_v2-1024x972.png","datePublished":"2023-09-12T08:14:56+00:00","dateModified":"2026-01-26T15:14:21+00:00","breadcrumb":{"@id":"https:\/\/sites.uef.fi\/bioinformatics\/services\/#breadcrumb"},"inLanguage":"en-US","potentialAction":[{"@type":"ReadAction","target":["https:\/\/sites.uef.fi\/bioinformatics\/services\/"]}]},{"@type":"ImageObject","inLanguage":"en-US","@id":"https:\/\/sites.uef.fi\/bioinformatics\/services\/#primaryimage","url":"https:\/\/sites.uef.fi\/bioinformatics\/wp-content\/uploads\/sites\/425\/2025\/03\/bic_v2.png","contentUrl":"https:\/\/sites.uef.fi\/bioinformatics\/wp-content\/uploads\/sites\/425\/2025\/03\/bic_v2.png","width":1636,"height":1553},{"@type":"BreadcrumbList","@id":"https:\/\/sites.uef.fi\/bioinformatics\/services\/#breadcrumb","itemListElement":[{"@type":"ListItem","position":1,"name":"Home","item":"https:\/\/sites.uef.fi\/bioinformatics\/"},{"@type":"ListItem","position":2,"name":"Analysis Services"}]},{"@type":"WebSite","@id":"https:\/\/sites.uef.fi\/bioinformatics\/#website","url":"https:\/\/sites.uef.fi\/bioinformatics\/","name":"UEF Bioinformatics Center","description":"","potentialAction":[{"@type":"SearchAction","target":{"@type":"EntryPoint","urlTemplate":"https:\/\/sites.uef.fi\/bioinformatics\/?s={search_term_string}"},"query-input":{"@type":"PropertyValueSpecification","valueRequired":true,"valueName":"search_term_string"}}],"inLanguage":"en-US"}]}},"_links":{"self":[{"href":"https:\/\/sites.uef.fi\/bioinformatics\/wp-json\/wp\/v2\/pages\/224","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/sites.uef.fi\/bioinformatics\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/sites.uef.fi\/bioinformatics\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/sites.uef.fi\/bioinformatics\/wp-json\/wp\/v2\/users\/990"}],"replies":[{"embeddable":true,"href":"https:\/\/sites.uef.fi\/bioinformatics\/wp-json\/wp\/v2\/comments?post=224"}],"version-history":[{"count":1,"href":"https:\/\/sites.uef.fi\/bioinformatics\/wp-json\/wp\/v2\/pages\/224\/revisions"}],"predecessor-version":[{"id":1489,"href":"https:\/\/sites.uef.fi\/bioinformatics\/wp-json\/wp\/v2\/pages\/224\/revisions\/1489"}],"wp:attachment":[{"href":"https:\/\/sites.uef.fi\/bioinformatics\/wp-json\/wp\/v2\/media?parent=224"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}