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Introduction to R/RStudio Patrick Kimes, PhD Postdoctoral Fellow Dana-Farber Cancer Institute Harvard TH Chan School of Public Health Top Ten Seminars October 1, 2019

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October 1, 2019 October 22, 2019 November 12, 2019 December 10, 2019 January 21, 2020 February 11, 2020 March 17, 2020 April 14, 2020 May 19, 2020 June 16, 2020 Introduction to R and RStudio Data visualization with ggplot2 Data visualization principles and plots to avoid Design of Clinical Trials Basics Correlation: you are probably using it wrong How to detect and deal with batch effects Brief introduction to machine learning Culprits of the reproducibility crisis: multiple testing and p-hacking Experimental Design: How many size and should I pool? Detecting differentially expressed genes with RNA-seq top ten seminars in data science

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R and RStudio?

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R and RStudio? programming language R think Java, C, C++, Python, …

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RStudio programming language R and RStudio? software to make data analysis with R easier

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RStudio programming language R and RStudio? programming language R software to make data analysis with R easier

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RStudio engine R dashboard

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why R and RStudio?

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what about SAS? why R and RStudio?

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what about SAS? • R is free, open source • R is the home of new methods • R has a large, active community • R is highly interoperable, extensible why R and RStudio?

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what about Python? why R and RStudio?

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what about Python? • Good question! Up to you! • R is arguably easier to learn • R has more statistical tools • R makes exploration and visualization easier why R and RStudio?

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why R and RStudio?

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it gets you to the data fast! why R and RStudio?

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it gets you to the data fast! and that’s fun! https://twitter.com/avogado6/status/1165595520967954432

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who already has R / RStudio installed?

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how to install R and RStudio

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how to install R and RStudio 1. Search “R”, 
 Search “RStudio” 2. Install “R”, 
 Install “RStudio”

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how to install R and RStudio 1. Search “R”, 
 Search “RStudio” 2. Install “R”, 
 Install “RStudio” maybe a few more steps so please do this later a much better guide: rafalab.github.io/dsbook/installing-r-rstudio

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lucky us! we have a workaround! https://rstudio.cloud

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lucky us! we have a workaround! https://rstudio.cloud do this

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lucky us! we have a workaround! https://rstudio.cloud this too

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lucky us! we have a workaround! https://rstudio.cloud select [from Git repo]

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lucky us! we have a workaround! https://rstudio.cloud enter https://github.com/pkimes/dfci-introR

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welcome to RStudio!

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local RStudio select [New Project]

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local RStudio select [Version Control]

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local RStudio we’ll use [Git]

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local RStudio enter https://github.com/pkimes/dfci-introR

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we’re good to go!

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you now have a project! what’s an RStudio project? basically a folder to organize an analysis • input data • R scripts • results/figures

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coding coding coding coding coding coding coding coding coding coding coding coding coding coding coding coding coding coding coding coding let’s give it a try!

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arithmetic variables functions help installing packages loading packages for-loops what did we (hopefully) cover?

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some pieces in the modern (R) data scientist’s toolbox

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some pieces in the modern (R) data scientist’s toolbox rmarkdown tidyverse shiny [bioconductor] documentation, communication data manipulation, visualization web application framework community of genomics packages

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some pieces in the modern (R) data scientist’s toolbox rmarkdown tidyverse shiny [bioconductor] documentation, communication data manipulation, visualization web application framework community of genomics packages

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.R file

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.R file .Rmd file

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.R file .Rmd file formal header

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.R file .Rmd file code “chunks”

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.R file .Rmd file plain text (markdown)

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.R file .Rmd file specified output format

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.Rmd file

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.Rmd file formatted text output! R code

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rmarkdown documentation, communication myfile.Rmd markdown + R code chunks

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rmarkdown documentation, communication myfile.Rmd markdown + R code chunks markdown myfile.md execute R code

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rmarkdown documentation, communication myfile.Rmd markdown + R code chunks markdown myfile.md execute R code pandoc conversion

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rmarkdown documentation, communication rmarkdown.rstudio.com

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coding coding coding coding coding coding coding coding coding coding coding coding coding coding coding coding coding coding coding coding let’s give it a try!

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what did we (hopefully) cover? create a new Rmd file writing simple markdown creating code chunks executing code knitting documents

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some pieces in the modern (R) data scientist’s toolbox rmarkdown tidyverse shiny [bioconductor] documentation, communication data manipulation, visualization web application framework community of genomics packages

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some pieces in the modern (R) data scientist’s toolbox rmarkdown tidyverse shiny [bioconductor] documentation, communication data manipulation, visualization web application framework community of genomics packages

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tidyverse data manipulation, visualization tidyverse.org

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some pieces in the modern (R) data scientist’s toolbox rmarkdown tidyverse shiny [bioconductor] documentation, communication data manipulation, visualization web application framework community of genomics packages

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shiny web application framework shiny.rstudio.com

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shiny web application framework shiny.rstudio.com/gallery/kmeans-example

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some pieces in the modern (R) data scientist’s toolbox rmarkdown tidyverse shiny [bioconductor] documentation, communication data manipulation, visualization web application framework community of genomics packages

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bioconductor community of genomics packages bioconductor.org

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bioconductor community of genomics packages CRAN Bioconductor • genomic focus • software • annotations • data • package reviews • scope • consistency

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awesome!

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where do we go from here?

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where do we go from here? wait, I’m lost

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introduction to data science rafalab.github.io/dsbook

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RStudio Cloud tutorials rstudio.cloud

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r4ds.had.co.nz R for data science

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learn the tidyverse tidyverse.org/learn

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advanced R adv-r.hadley.nz

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biomedical data science open online training rafalab.github.io/pages/harvardx

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… and because it’s 2019, deep learning tensorflow.rstudio.com

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questions? wait, I’m still lost