This information is over 2 years old. Information was current at time of publication.{"id":4132,"date":"2021-03-28T14:46:21","date_gmt":"2021-03-28T19:46:21","guid":{"rendered":"http:\/\/info.hsls.pitt.edu\/molbio\/?p=4132"},"modified":"2021-04-12T10:28:11","modified_gmt":"2021-04-12T15:28:11","slug":"partek-flow-user-training-series","status":"publish","type":"post","link":"https:\/\/info.hsls.pitt.edu\/molbio\/2021\/03\/28\/partek-flow-user-training-series\/","title":{"rendered":"Partek Flow User Training Series"},"content":{"rendered":"<p>Learn how to analyze RNA-Seq &amp; Single Cell data using Partek Flow bioinformatics software in this user training series.<!--more--><\/p>\n<p><a href=\"https:\/\/www.partek.com\/training\/partek-flow-series\/\"><strong>Register Here<\/strong><\/a><\/p>\n<p><strong>Partek Flow Basic Components<\/strong> (90 mins)<br \/>\n30 March, 1pm<\/p>\n<ul>\n<li>How to transfer files to Flow server<\/li>\n<li>Import data to a project: \u2013 fastq, bam, bcl, .txt, .h5, seurat object \u2013 GEO project, URL, Basespace<\/li>\n<li>Sample attribute management<\/li>\n<li>Project management: \u2013 Task log, sharing, task details \u2013 Project and data export \u2013 Importing and re-using pipelines<\/li>\n<li>Library file management<\/li>\n<li>Gene list management<\/li>\n<li>Orphaned files cleaning<\/li>\n<\/ul>\n<p><strong>Bulk RNA-Seq Data Analysis<\/strong> (60 min)<br \/>\n1 April, 1pm<\/p>\n<ul>\n<li>QA\/QC<\/li>\n<li>Trimming bases and filtering reads<\/li>\n<li>Alignment<\/li>\n<li>Quantification<\/li>\n<li>Filtering features and normalization<\/li>\n<li>Differential analysis<\/li>\n<li>Alternative splicing detection<\/li>\n<li>Biological interpretation<\/li>\n<li>Data visualization: PCA scatterplot, volcano plot, heatmap, dot plot, chromosome view etc.<\/li>\n<\/ul>\n<p><strong>scRNA-Seq Data Analysis: Basic Functions for a Single Sample<\/strong> (60 mins)<br \/>\n6 April, 1pm<\/p>\n<ul>\n<li>Single cell QA\/QC \u2013 QC cells and filter \u2013 QC features and filter<\/li>\n<li>Normalization methods<\/li>\n<li>Dimension reduction methods- PCA, tSNE, UMAP<\/li>\n<li>Clustering analysis- Graph-based clustering- K-means clustering<\/li>\n<li>Cell type classification in Data Viewer<\/li>\n<li>Visualization: scatterplot, violin plot<\/li>\n<li>Trajectory analysis<\/li>\n<\/ul>\n<p><strong>scRNA-Seq Data Analysis: Advanced Functions for Multiple Samples<\/strong> (60 mins)<br \/>\n8 April, 1pm<\/p>\n<ul>\n<li>Batch removal methods<\/li>\n<li>Differential analysis<\/li>\n<li>Sample composition analysis<\/li>\n<li>Pseudo bulk analysis<\/li>\n<li>Visualization: dot plot, box plot, violin plot, volcano plot, heatmap, bubble map, bar chart, pie chart<\/li>\n<li>Spatial transcriptome<\/li>\n<li>CITE-Seq data analysis<\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>Learn how to analyze RNA-Seq &amp; Single Cell data using Partek Flow bioinformatics software in this user training series.<\/p>\n<p><a class=\"read-more\" alt= \"Partek Flow User Training Series\" href=\"https:\/\/info.hsls.pitt.edu\/molbio\/2021\/03\/28\/partek-flow-user-training-series\/\">Read more&hellip;<\/a><\/p>\n","protected":false},"author":31,"featured_media":274,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":"","_links_to":"","_links_to_target":""},"categories":[1],"tags":[],"class_list":["post-4132","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-uncategorized"],"_links":{"self":[{"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/posts\/4132","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/users\/31"}],"replies":[{"embeddable":true,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/comments?post=4132"}],"version-history":[{"count":3,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/posts\/4132\/revisions"}],"predecessor-version":[{"id":4135,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/posts\/4132\/revisions\/4135"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/media\/274"}],"wp:attachment":[{"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/media?parent=4132"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/categories?post=4132"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/tags?post=4132"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}