{"id":16317,"date":"2024-05-17T14:28:41","date_gmt":"2024-05-17T18:28:41","guid":{"rendered":"https:\/\/info.hsls.pitt.edu\/updatereport\/?p=16317"},"modified":"2024-05-23T22:41:03","modified_gmt":"2024-05-24T02:41:03","slug":"learn-hsls-single-cell-rna-seq-data-analysis-using-partek-flow","status":"publish","type":"post","link":"https:\/\/info.hsls.pitt.edu\/updatereport\/learn-hsls-single-cell-rna-seq-data-analysis-using-partek-flow\/","title":{"rendered":"Learn @ HSLS: Single Cell RNA-Seq Data Analysis using Partek Flow"},"content":{"rendered":"<p>Join us for this class:<br \/>\nWednesday, June 26, 1-4 p.m., Online<br \/>\nTaught by <a href=\"https:\/\/www.hsls.pitt.edu\/staff\/ansuman-chattopadhyay\">Ansuman Chattopadhyay<\/a> and <a href=\"https:\/\/www.hsls.pitt.edu\/staff\/sri-chaparala\">Srilakshmi Chaparala<\/a><br \/>\n<a href=\"https:\/\/www.hsls.pitt.edu\/instruction\/single-cell-rna-seq-data-analysis-using-partek-flow\/6503\">Register for Single Cell RNA-Seq Data Analysis using Partek Flow<\/a>*<\/p>\n<p>This workshop is on single cell RNA-Seq analysis with multiple samples using HSLS-licensed\u00a0<a href=\"https:\/\/hsls.libguides.com\/MBIStools\/partekflow\">Partek Flow\u00a0<\/a>software.<\/p>\n<p><strong>Target Audience:<\/strong>\u00a0Experimental biologists seeking to learn how to analyze the single cell data generated through experiments or retrieved from a publication or a repository such as GEO. The software covered in the workshop operates through a user-friendly, point-and-click graphical user interface, so neither computer programming experience nor familiarity with the command-line interface is required.<\/p>\n<p><!--more--><\/p>\n<p><strong>Upon completing this class, you should be able to:<\/strong><\/p>\n<ul>\n<li>analyze from raw data (FASTQ files)<\/li>\n<li>import FASTQ files and run Cellranger software to generate single cell count matrix<\/li>\n<li>analyze from count matrix data<\/li>\n<li>import single cell count matrix<\/li>\n<li>perform quality checks (QC) on single cell data<\/li>\n<li>filter and normalize the data<\/li>\n<li>generate PCA, t-SNE, and UMAP plots to visualize data<\/li>\n<li>identify cell populations and biomarkers in the multi-sample data<\/li>\n<li>compute differential gene expressions between two cell populations\u202fand\/or samples<\/li>\n<\/ul>\n<p><strong>Level: <\/strong>Novice<\/p>\n<p><strong>What should you do before attending this class: <\/strong>Register for\u00a0<a href=\"https:\/\/hsls.libguides.com\/MBISsoftware\/partekflow\">Partek Flow<\/a>\u00a0software.<\/p>\n<p><strong>Recording status: <\/strong>This class will be recorded and shared with attendees.<\/p>\n<p><strong>Class Materials: <\/strong>Class materials will be shared with attendees.<\/p>\n<p>If you are unable to attend this scheduled class, consider <a href=\"https:\/\/www.hsls.pitt.edu\/group-course-instruction\">requesting a customized instruction session<\/a> for your course, group, or department.<\/p>\n<p>*HSLS classes are open to University of Pittsburgh faculty, staff, and students, as well as UPMC residents and fellows.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Join us for this class: Wednesday, June 26, 1-4 p.m., Online Taught by Ansuman Chattopadhyay and Srilakshmi Chaparala Register for Single Cell RNA-Seq Data Analysis using Partek Flow* This workshop is on single cell RNA-Seq analysis with multiple samples using HSLS-licensed\u00a0Partek Flow\u00a0software. Target Audience:\u00a0Experimental biologists seeking to learn how to analyze the single cell data [&hellip;]<\/p>\n","protected":false},"author":46,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"issue-archives","meta":{"footnotes":"","_links_to":"","_links_to_target":""},"categories":[210],"tags":[-1],"class_list":["post-16317","post","type-post","status-publish","format-standard","hentry","category-june-2024","avhec_catgroup-issue-archives"],"_links":{"self":[{"href":"https:\/\/info.hsls.pitt.edu\/updatereport\/wp-json\/wp\/v2\/posts\/16317","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/info.hsls.pitt.edu\/updatereport\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/info.hsls.pitt.edu\/updatereport\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/info.hsls.pitt.edu\/updatereport\/wp-json\/wp\/v2\/users\/46"}],"replies":[{"embeddable":true,"href":"https:\/\/info.hsls.pitt.edu\/updatereport\/wp-json\/wp\/v2\/comments?post=16317"}],"version-history":[{"count":5,"href":"https:\/\/info.hsls.pitt.edu\/updatereport\/wp-json\/wp\/v2\/posts\/16317\/revisions"}],"predecessor-version":[{"id":16355,"href":"https:\/\/info.hsls.pitt.edu\/updatereport\/wp-json\/wp\/v2\/posts\/16317\/revisions\/16355"}],"wp:attachment":[{"href":"https:\/\/info.hsls.pitt.edu\/updatereport\/wp-json\/wp\/v2\/media?parent=16317"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/info.hsls.pitt.edu\/updatereport\/wp-json\/wp\/v2\/categories?post=16317"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/info.hsls.pitt.edu\/updatereport\/wp-json\/wp\/v2\/tags?post=16317"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}