{"id":5797,"date":"2026-03-20T08:35:09","date_gmt":"2026-03-20T13:35:09","guid":{"rendered":"https:\/\/info.hsls.pitt.edu\/molbio\/?p=5797"},"modified":"2026-04-02T08:40:46","modified_gmt":"2026-04-02T13:40:46","slug":"learn-hsls-chat-to-code-in-r-bulk-rna-seq-in-google-colab-with-generative-ai-march-25","status":"publish","type":"post","link":"https:\/\/info.hsls.pitt.edu\/molbio\/2026\/03\/20\/learn-hsls-chat-to-code-in-r-bulk-rna-seq-in-google-colab-with-generative-ai-march-25\/","title":{"rendered":"Learn @ HSLS: Chat to Code in R: Bulk RNA-Seq in Google Colab with Generative AI, March 25"},"content":{"rendered":"<p>Wednesday, March 25, 2026, 1-3 p.m., Online<br \/>\nTaught by Srilakshmi Chaparala and Alexis Cenname<br \/>\n<a href=\"https:\/\/www.hsls.pitt.edu\/instruction\/data-science\/chat-code-r-bulk-rna-seq-google-colab-generative-ai\/13296\">Register for Chat to Code in R: Bulk RNA-Seq in Google Colab with Generative AI<\/a><\/p>\n<div class=\"field field--name-body field--type-text-with-summary field--label-hidden field__item\">\n<p>Turn plain\u2011English prompts into reproducible R code as we walk through the key steps of a bulk RNA\u2011seq analysis\u2014no prior coding knowledge required. In this hands-on session, you\u2019ll start with raw RNA-seq count data downloaded from a GEO-deposited study and work through quality control, differential expression between two conditions (using DESeq2 and edgeR), publication-ready visualizations (volcano plots, heatmaps, MA plots), and functional enrichment to interpret pathways and biology. The core of the workshop is a chat-based, prompt-driven workflow: you\u2019ll learn how to describe your intent in natural language and have R code generated for you, then run, refine, and document it using Google Colab. Along the way, we\u2019ll cover data upload, environment setup, effective prompt writing, and result interpretation.<\/p>\n<\/div>\n<p><!--more--><\/p>\n<div class=\"field field--name-field-learning-objective field--type-string field--label-above\">\n<div class=\"field__label\"><strong>Upon completing this class, you should be able to:<\/strong><\/div>\n<ul class=\"field field--name-field-learning-objective field--type-string field--label-above field__items\">\n<li class=\"field__item\">Summarize the bulk RNA\u2011seq analysis pipeline (raw count data \u2192 QC\/PCA \u2192 DEGs \u2192 enrichment) and define key concepts (normalization, dispersion, multiple testing, contrasts)<\/li>\n<li class=\"field__item\">Formulate effective chat-based prompts using Google Gemini to generate R code for RNA-seq data analysis workflow<\/li>\n<li class=\"field__item\">Perform differential expression with DESeq2 and edgeR, and compare outputs (e.g., DEG counts, log2FC, adjusted p\u2011values<\/li>\n<li class=\"field__item\">Assemble a reproducible Colab notebook that documents prompts, generated R code, and results (DEG tables, plots, enrichment summaries), suitable for reuse and reporting.<\/li>\n<\/ul>\n<\/div>\n<div class=\"field field--name-field-class-level field--type-list-string field--label-inline\">\n<div class=\"field__label\"><strong>Level:<\/strong> Novice<\/div>\n<\/div>\n<div><\/div>\n<div>\n<div class=\"field field--name-field-class-prerequisites field--type-text-long field--label-inline\">\n<div class=\"field__label\"><strong>Prerequisites:<\/strong> We recommend that you complete\u00a0<a href=\"https:\/\/pitt.hosted.panopto.com\/Panopto\/Pages\/Viewer.aspx?id=0e1cb403-bb10-4fa7-8b40-b31301238873\">R Bootcamp Session 1; Lecture Video<\/a><\/div>\n<div><\/div>\n<\/div>\n<div class=\"field field--name-field-pre-work-description field--type-text-long field--label-inline\">\n<div class=\"field__label\"><strong>Recording status:<\/strong> This class will be recorded and shared with attendees.<\/div>\n<\/div>\n<\/div>\n<div class=\"field field--name-field-class-materials field--type-list-string field--label-inline\">\n<div><\/div>\n<div class=\"field__label\"><strong>Class Materials:<\/strong> Class materials will be shared with attendees.<\/div>\n<\/div>\n","protected":false},"excerpt":{"rendered":"<p>Wednesday, March 25, 2026, 1-3 p.m., Online<br \/>\nTaught by Srilakshmi Chaparala and Alexis Cenname<br \/>\n<a href=\"https:\/\/www.hsls.pitt.edu\/instruction\/data-science\/chat-code-r-bulk-rna-seq-google-colab-generative-ai\/13296\">Register for Chat to Code in R: Bulk RNA-Seq in Google Colab with Generative AI<\/a><\/p>\n<p>Turn plain\u2011English prompts into reproducible R code as we walk through the key steps of a bulk RNA\u2011seq analysis\u2014no prior coding knowledge required.<\/p>\n<p><a class=\"read-more\" alt= \"Learn @ HSLS: Chat to Code in R: Bulk RNA-Seq in Google Colab with Generative AI, March 25\" href=\"https:\/\/info.hsls.pitt.edu\/molbio\/2026\/03\/20\/learn-hsls-chat-to-code-in-r-bulk-rna-seq-in-google-colab-with-generative-ai-march-25\/\">Read more&hellip;<\/a><\/p>\n","protected":false},"author":46,"featured_media":5724,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":"","_links_to":"","_links_to_target":""},"categories":[65],"tags":[],"class_list":["post-5797","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-march-2026"],"_links":{"self":[{"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/posts\/5797","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\/46"}],"replies":[{"embeddable":true,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/comments?post=5797"}],"version-history":[{"count":1,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/posts\/5797\/revisions"}],"predecessor-version":[{"id":5798,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/posts\/5797\/revisions\/5798"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/media\/5724"}],"wp:attachment":[{"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/media?parent=5797"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/categories?post=5797"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/info.hsls.pitt.edu\/molbio\/wp-json\/wp\/v2\/tags?post=5797"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}