Course Modules
Learn R - Introduction to R features and syntax
Learn R - Introduction to R features and syntax
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Assignment1 - Do : R basics with Swirl interactive tutorial 1 - Do : R basics with Swirl interactive tutorialScore at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
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Attachment2025-01-13-Intro-and-Hwk1.pdf 2025-01-13-Intro-and-Hwk1.pdfScore at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Learn R - Markdown
Learn R - Markdown
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Assignment2 - Do : Make a Markdown document 2 - Do : Make a Markdown documentScore at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
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External UrlGetting Started with R Markdown — Guide and Cheatsheet Getting Started with R Markdown — Guide and CheatsheetScore at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
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External UrlLiterate Programming : Introduction to Markdown from Prof. Danielle Navarro Literate Programming : Introduction to Markdown from Prof. Danielle NavarroScore at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
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External UrlLiterate Programming : Curated and hyperlinked abstracts from literature about literate programming Literate Programming : Curated and hyperlinked abstracts from literature about literate programmingScore at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
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External UrlData Visualization: Scatterplots Youtube Walkthrough Data Visualization: Scatterplots Youtube WalkthroughScore at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
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AttachmentDemo.Rmd Demo.RmdScore at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
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AttachmentDemo.html Demo.htmlScore at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Learn R - Vectors, Lists and Looping functions
Learn R - Vectors, Lists and Looping functions
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Assignment3 - Do : Vectors, Lists and Looping functions 3 - Do : Vectors, Lists and Looping functionsScore at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
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Attachment2025-02-03-VectorsListsLoopingFunctionsHW3.pdf 2025-02-03-VectorsListsLoopingFunctionsHW3.pdfScore at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Learn Why - Reproducible research matters
Learn Why - Reproducible research matters
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Assignment3.5 - Do : Learn about reproducible research and research ethics 3.5 - Do : Learn about reproducible research and research ethicsScore at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
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PageWatch: Dr. Keith Baggerly describes how he and his colleagues discovered a problem affecting patients seeking cancer care Watch: Dr. Keith Baggerly describes how he and his colleagues discovered a problem affecting patients seeking cancer careScore at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
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External UrlRead: The five pillars of computational reproducibility: bioinformatics and beyond (literate programming section) Read: The five pillars of computational reproducibility: bioinformatics and beyond (literate programming section)Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
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External UrlRead: Officials Silenced Med Student Who Reported Trouble (Cancer Letter, January 9, 2015) Read: Officials Silenced Med Student Who Reported Trouble (Cancer Letter, January 9, 2015)Score at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
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External UrlRead: On being a scientist: A guide to responsible conduct of research, 3rd edition Read: On being a scientist: A guide to responsible conduct of research, 3rd editionScore at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Learn R - Matrices, Plots, P hacking
Learn R - Matrices, Plots, P hacking
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Assignment4 - Do : Matrices, plots, p hacking 4 - Do : Matrices, plots, p hackingScore at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
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Attachment2025-02-17-SubsettingSubcripting.pdf 2025-02-17-SubsettingSubcripting.pdfScore at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Learn about single-cell RNA-Seq experiments
Learn about single-cell RNA-Seq experiments
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Assignment4.5 - Do: Learn about single-cell RNA-Seq experiments and data 4.5 - Do: Learn about single-cell RNA-Seq experiments and dataScore at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Learn R - S3 and S4 classes, Object-oriented programming in R
Learn R - S3 and S4 classes, Object-oriented programming in R
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Attachment2025-03-17-OOP-in-R-S3S4Classes.pdf 2025-03-17-OOP-in-R-S3S4Classes.pdfScore at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
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Attachment9-ObjectOrientedProgramming.pdf 9-ObjectOrientedProgramming.pdfScore at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
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Assignment5 - Do : S3 classes, S4 classes 5 - Do : S3 classes, S4 classesScore at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Learn or explain complex data analysis library - Seurat
Learn or explain complex data analysis library - Seurat
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Assignment6 - Do : Learn the Seurat library for single-cell RNA-Seq data analysis and visualization 6 - Do : Learn the Seurat library for single-cell RNA-Seq data analysis and visualizationScore at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
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Attachment2025-03-24-single-cell-rna-seq.pdf 2025-03-24-single-cell-rna-seq.pdfScore at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
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Attachment2025-03-31-Markdown-Walkthrough.pdf 2025-03-31-Markdown-Walkthrough.pdfScore at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Project - Answer a question about biology using R and data
Project - Answer a question about biology using R and data
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Attachment2025-04-07-Projects.pdf 2025-04-07-Projects.pdfScore at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
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Assignment6.25 - Do : Choose Term Project 6.25 - Do : Choose Term ProjectScore at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
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Assignment6.5 - Do : First draft of Term Project 6.5 - Do : First draft of Term ProjectScore at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
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Assignment7 - Do : Term project 7 - Do : Term projectScore at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
Dimensionality Reduction and Hierarchical Clustering
Dimensionality Reduction and Hierarchical Clustering
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Assignment8 - Do : Swirl tutorials on dimension reduction and clustering 8 - Do : Swirl tutorials on dimension reduction and clusteringScore at least Must score at least to complete this module item Scored at least Module item has been completed by scoring at least Score at least % Must score at least % to complete this module item Scored at least % Module item has been completed by scoring at least % View Must view in order to complete this module item Viewed Module item has been viewed and is complete Mark done Must mark this module item done in order to complete Marked done Module item marked as done and is complete Contribute Must contribute to this module item to complete it Contributed Contributed to this module item and is complete Submit Must submit this module item to complete it Submitted Module item submitted and is complete
