# JMU CGEMS 2021 Workshop: Getting Started with R and CyVerse

- **Instructor**: Jason Williams, Cold Spring Harbor Laboratory/CyVerse, [e-mail], @JasonWilliamsNY (twitter)
- **Organizer**: Karen Barnard-Kubow, James Madison University, [e-mail]

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## Schedule and connection info

- Zoom link: https://cshl-dnalc.zoom.us/j/92877843079
- Zoom meeting ID: 928 7784 3079

- **June 28** 9:30AM - 1:30PM (Eastern)
- **June 29** 9:30AM - 1:30PM (Eastern)
- **June 30** 9:30AM - 1:30PM (Eastern)
- **July 01** 9:30AM - 1:30PM (Eastern)

Main break at 11:30 - 11:50; stretch breaks 10:30/12:45

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## Workshop Links/Materials

We will be using materials from a variety of sources, here they are for quick reference.

*Code of Conduct*
- CyVerse Code of Conduct: https://learning.cyverse.org/projects/cyverse-foss/en/latest/getting_started/code_of_conduct.html

*Instant Feedback*

- Google form: https://forms.gle/zidCpe6HvdwXRbJv8

*Platform links*
- CyVerse User Portal (account management):https://user.cyverse.org/
- CyVerse Discovery Enviornment: https://de.cyverse.org/
- CyVerse Learning Center: https://learning.cyverse.org/en/latest/
- VICE R application:https://de.cyverse.org/apps/de/95476bc6-bbe3-11eb-a080-008cfa5ae621
- Atmosphere: https://atmo.cyverse.org/application

*Software Downloads (optional)*
- Cyberduck (available for Windows/MacOS):https://cyberduck.io/download/
- iCommands
- RStudio (Desktop, free): https://www.rstudio.com/products/rstudio/
- R (binaries): https://cran.r-project.org/

*Example data downloads*

- Data Store Path: /iplant/home/shared/cyverse_training/workshop_materials/cgems_2021

- R Ecology data: https://doi.org/10.6084/m9.figshare.1314459
- R Genomics data:
- combined_tidy: https://data.cyverse.org/dav-anon/iplant/projects/cyverse_training/workshop_materials/cgems_2021/r_ecology/portal_data_joined.csv
- Ecoli metadata: https://data.cyverse.org/dav-anon/iplant/projects/cyverse_training/workshop_materials/cgems_2021/r_genomics/Ecoli_metadata.xlsx

*Primary Learning Materials*

CyVerse

- Discovery Enviornment guide: https://learning.cyverse.org/projects/cyverse-de2-guide/en/latest/
- Data store guide: https://cyverse-data-store-guide.readthedocs-hosted.com/en/latest/
- RNA-Seq tutorial: https://learning.cyverse.org/projects/kallisto_tutorial/en/latest/step3.html?highlight=kallisto#analyze-kallisto-results-with-sleuth

R
- Data Carpentry R Genomics Intro: https://datacarpentry.org/genomics-r-intro/
- Data Carpentry R Ecology Intro: https://datacarpentry.org/R-ecology-lesson/
- Data Carpentry R Tidyverse: https://datacarpentry.org/R-ecology-lesson/03-dplyr.html
- Data Carpentry Visualization with ggplot2: https://datacarpentry.org/R-ecology-lesson/04-visualization-ggplot2.html
- Docker Quickstart: https://learning.cyverse.org/projects/cyverse-creating-docker-containers-quickstart/en/latest/

*Other learning links*
(Feel free to add)

- R For Data Science: https://r4ds.had.co.nz/
- TidyVerse refference: https://www.tidyverse.org/packages/
- R Cookbook: http://www.cookbook-r.com/
- STHDA ggplot2 essentials: http://www.sthda.com/english/wiki/ggplot2-essentials
- ggplot2 book: https://ggplot2-book.org/index.html
- Bioinformatics.ca intro to R workshop: https://www.youtube.com/watch?v=Qf83W1ki_2M&list=PL3izGL6oi0S8hCNFASxO2EOINJF3W6v4A

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## Day I: Introduction to CyVerse

Sign in:
- Consuelo Alvarez, Longwood University, [e-mail]
- Jason Williams, CSHL
- Terrie Rife, JMU, [e-mail]
- Kianna Butts, JMU [e-mail]
- Emily Butters, JMU [e-mail]
- Tyler Gandee, JMU, [e-mail]
- Chris Rose, JMU, [e-mail]
- Ian McNeil, Bridgewater College Chemistry Dept., [e-mail]
- Ken Overway, Bridgewater College Chemistry Dept., [e-mail]
- Steve Baron, Bridgewater College, Biology Dept.
- Jaira Ferreira de Vasconcellos, JMU, [e-mail]
- Deva O'Neil, Bridgewater / Physics, doneil at bridgewater.edu
- Melissa Hoover, Bridgewater College, math and CS, [e-mail]
- Laura Lambert, JMU, [e-mail]
- Chrisi Hughey, JMU, [e-mail]
- Kim Bolyard, Bridgewater College, [e-mail]
- Ron Phillips, JMU, [e-mail]
- Kris Kubow, JMU, [e-mail]
- Karen Kubow, JMU
- Rebecca Simmons, JMU, [e-mail]
- Diana Hsieh, UA, [e-mail]
- Karina Medina-Jimenez, Arkansas State University, [e-mail]
- Grace Wyngaard, [e-mail]
- Chulantha Diyes, [e-mail], University of Saskatchewan
- R. Paul Evans, [e-mail], Brigham Young University
- - Grace Wyngaard, [e-mail]

**Notes**

- Question box:

### Breakout Rooms/Topics

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## Day II: Introduction to R

Sign in:
- Jason Williams, CSHL
- Karen Barnard-Kubow, JMU
- Chrisi Hughey, JMU, Chemistry, [e-mail]
- Chris Rose, JMU, Biology
- Ken Overway, Bridgewater College, [e-mail]
- Consuelo Alvarez. Longwood University
- Laura Lambert, JMU, [e-mail]
- Kris Kubow, JMU
- Melissa Hoover, Bridgewater College, math and CS department, [e-mail]
- Stephen Baron, Bridgewater College Biology
- Rebecca Simmons, JMU, [e-mail]
- Diana Hsieh, UA, [e-mail]
- Kianna Butts, JMU
- Deva O'Neil BC Physics
- Patrice Ludwig, JMU Biology, [e-mail]
- Ian McNeil, Bridgewater College Chemistry Dept., [e-mail]
- Jaira Ferreira de Vasconcellos, JMU, [e-mail]
- Karina Medina-Jimenez, Arkansas State University, [e-mail]
- Chulantha Diyes, University of Saskatchewan, Canada
- Terrie Rife, JMU
- Connor Murray, University of Virginia, [e-mail]
- Tyler Gandee, JMU
- Kim Bolyard, Bridgewater College
- R. Paul Evans, Brigham Young University

**Notes**

* R code for downloading the VCF spreasheet*

**Questions**

### Breakout Rooms/Topics
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## Day III: TidyVerse and ggplot2

Sign in:

- Jason Williams, CSHL
- Karen Barnard-Kubow, JMU
- Kianna Butts, JMU
- Ian McNeil, Bridgewter College Chemistry, [e-mail]
- Ken Overway, Bridgewater College, [e-mail]
- Laura Lambert, JMU, [e-mail]
- Melissa Hoover, Bridgewater College, Math & CS, [e-mail]
- -Grace Wyngaard, James Madison University, [e-mail]
- Chris Rose, Biology, JMU
- Kris Kubow, JMU
- Patrice Ludwig, JMU Biology, [e-mail]
- Jaira Ferreira de Vasconcellos, JMU, [e-mail]
- Tyler gandee , JMU
- Kim Bolyard, Bridgewater College
- Rebecca Simmons, JMU
- R. Paul Evans, Brigham Young University
- Chrisi Hughey, JMU, Chemistry, [e-mail]
-
-

**Notes**:

download.file("https://data.cyverse.org/dav-anon/iplant/projects/cyverse_training/workshop_materials/cgems_2021/r_genomics/combined_tidy_vcf.csv",
destfile = "combined_tidy_vcf.csv")

varients <- read.csv("combined_tidy_vcf.csv")

**import ecology data**

\# Import the dataset
download.file("https://data.cyverse.org/dav-anon/iplant/projects/cyverse_training/workshop_materials/cgems_2021/r_ecology/portal_data_joined.csv",
destfile ="portal_data_joined.csv" )

\# Install tidyverse package
install.packages("tidyverse")

### Breakout Rooms/Topics
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## Day IV: CyVerse and R in teaching

Sign in:

- Jason Williams, CSHL
- Karen Barnard-Kubow, JMU
- Ken Overway, Bridgewater College, [e-mail]
- Kris Kubow, JMU
- Kianna Butts, JMU
- Patrice Ludwig, JMU Biology, [e-mail]
- -Grace Wyngaard - JMU [e-mail]
- Chrisi Hughey, JMU, Chemistry, [e-mail]
- Ian McNeil, Bridgewater College, Chemistry, [e-mail]
- Rebecca Simmons, JMU, Integrated Science & Technology, [e-mail]
- Laura Lambert, JMU, [e-mail]
- Kim Bolyard, Bridgewater College
- Jaira Ferreira de Vasconcellos, JMU, [e-mail]
- Chris Rose, JMU, Biology
- R. Paul Evans, Brigham Young University, [e-mail]

Data for ggplot

# Import data from server
download.file("https://data.cyverse.org/dav-anon/iplant/projects/cyverse_training/workshop_materials/cgems_2021/r_ecology/surveys.csv",
destfile ="surveys.csv" )

# Another data set.....

download.file("https://data.cyverse.org/dav-anon/iplant/projects/cyverse_training/workshop_materials/cgems_2021/r_ecology/surveys_complete.csv",
destfile ="surveys_complete.csv" )

surveys_complete2 <- read_csv("surveys_complete.csv")

### Breakout Rooms/Topics
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