• About this Book
    • Skills Level
    • AnVIL Collection
  • Learning Objectives
  • Demo Chapters
  • 1 Introduction
    • 1.1 Motivation
    • 1.2 Target Audience
    • 1.3 Curriculum
  • 2 A new chapter
    • 2.1 Learning Objectives
    • 2.2 Libraries
    • 2.3 Subtopic
      • 2.3.1 Code examples
      • 2.3.2 Image example
      • 2.3.3 Video examples
      • 2.3.4 Links to files
      • 2.3.5 Links to websites
      • 2.3.6 Citation examples
      • 2.3.7 Callout boxes
      • 2.3.8 Dropdown summaries
    • 2.4 Print out session info
  • 3 AnVIL Module Library
    • 3.1 Include using cow::borrow_chapter()
    • 3.2 Background Highlighting for Borrowed Chapters
  • 4 Student Guide
    • 4.1 Activity One
    • 4.2 Activity Two
  • AnVIL Modules
  • 5 Workspaces
    • 5.1 Clone a Workspace
    • 5.2 Create a Workspace
    • 5.3 Open a Workspace
    • 5.4 Share a Workspace
  • 6 Billing
    • 6.1 Create Google Billing Account
    • 6.2 Add Terra to Google Billing Account
    • 6.3 Add Members to Google Billing Account
    • 6.4 Set Alerts for Google Billing
    • 6.5 View Spend for Google Billing
    • 6.6 Create Terra Billing Project
    • 6.7 Add Member to Terra Billing Project
    • 6.8 Disable Terra Billing Project
  • 7 Onboarding
    • 7.1 Create Google Account
  • 8 Using programming platforms on AnVIL
    • 8.1 Video overview on using Jupyter Notebooks
    • 8.2 Launching Jupyter
    • 8.3 Video overview on using Galaxy
    • 8.4 Starting Galaxy
    • 8.5 Navigating Galaxy
    • 8.6 Deleting Galaxy
    • 8.7 Video overview on using RStudio
    • 8.8 Launching RStudio
    • 8.9 Touring RStudio
    • 8.10 Pausing RStudio
    • 8.11 Deleting RStudio
    • 8.12 Pausing vs. Deleting cloud environments
      • 8.12.1 Generic cloud environment, with PD details
      • 8.12.2 RStudio, with no PD details
  • 9 Data modules
    • 9.1 Getting Data from HPC to AnVIL
  • 10 Student instructions
    • 10.1 Student Account Setup
    • 10.2 Student instructions for cloning a Workspace
      • 10.2.1 With no variables set:
      • 10.2.2 With variables set:
    • 10.3 Student instructions for launching Jupyter
      • 10.3.1 Using default Jupyter environment:
      • 10.3.2 Using custom Jupyter environment:
    • 10.4 Student instructions for launching RStudio
      • 10.4.1 Using default RStudio environment:
      • 10.4.2 Using custom RStudio environment:
  • 11 User Management
    • 11.1 Create Terra Group
    • 11.2 Add Member to Terra Group
    • 11.3 Find Group Email
  • 12 Why AnVIL
    • 12.1 Why AnVIL for Instructors?
  • 13 Why use AnVIL?
    • 13.1 Benefits of using AnVIL for research
      • 13.1.1 Ease of platform access
      • 13.1.2 Variety of analysis solutions
      • 13.1.3 Data: yours or cloud-hosted open & controlled access
      • 13.1.4 Data & analysis in same place
      • 13.1.5 Scalability
      • 13.1.6 Rent needed resources
      • 13.1.7 Role-based permissions
      • 13.1.8 Shareable workspaces
      • 13.1.9 Repository compliant with DMS Policy
    • 13.2 Benefits of using AnVIL in the classroom
    • 13.3 Overall benefits of AnVIL
      • 13.3.1 Ability to control costs
      • 13.3.2 Work with protected data safely
      • 13.3.3 Maintenance is handled
      • 13.3.4 Training and support is available
      • 13.3.5 Collaborative community
    • 13.4 Conclusion
  • 14 Instructor modules
    • 14.1 Why AnVIL for Instructors?
    • 14.2 Checklist Link
    • 14.3 Checklist Timeline (premade content)
    • 14.4 Recommendation to use STRIDES
  • 15 Status of Book Repositories in the AnVIL Collection
  • About the Authors
  • 16 References
  • This content was published with bookdown by:

    The Fred Hutch Data Science Lab

    Style adapted from: rstudio4edu-book (CC-BY 2.0)

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AnVIL Book Name

Chapter 15 Status of Book Repositories in the AnVIL Collection

Repo name Render/Package Status Number of Open Issues Number of branches Number of Open PRs Website up?
jhudsl/AnVIL_Template Render all output courses Open Issues GitHub Branches Open PRs Website Status
jhudsl/AnVIL_Book_Getting_Started Render all output courses Open Issues GitHub Branches Open PRs Website Status
fhdsl/AnVIL_Demos Render all output courses Open Issues GitHub Branches Open PRs Website Status
fhdsl/AnVIL_Collection Render all output courses Open Issues GitHub Branches Open PRs Website Status
jhudsl/AnVIL_Book_WDL Render all output courses Open Issues GitHub Branches Open PRs Website Status
fhdsl/AnVIL_SRA_Data Render all output courses Open Issues GitHub Branches Open PRs Website Status
fhdsl/AnVIL_Data_Subsetting Render all output courses Open Issues GitHub Branches Open PRs Website Status
fhdsl/Data_on_AnVIL Render all output courses Open Issues GitHub Branches Open PRs Website Status
jhudsl/AnVIL_Book_Champions Render all output courses Open Issues GitHub Branches Open PRs Website Status
jhudsl/AnVIL_Book_Instructor_Guide Render all output courses Open Issues GitHub Branches Open PRs Website Status
fhdsl/AnVIL_Book_Epigenetics_Intro Render all output courses Open Issues GitHub Branches Open PRs Website Status
jhudsl/AnVIL_Phylogenetic-Techniques Render all output courses Open Issues GitHub Branches Open PRs Website Status
fhdsl/AnVIL_Urban_Genomics_PCA Render all output courses Open Issues GitHub Branches Open PRs Website Status
fhdsl/GDSCN_BioDIGS_Book Render all output courses Open Issues GitHub Branches Open PRs Website Status
fhdsl/GDSCN_BioDIGS_Soil Render all output courses Open Issues GitHub Branches Open PRs Website Status
fhdsl/GDSCN_BioDIGS_AMR Render all output courses Open Issues GitHub Branches Open PRs Website Status
fhdsl/GDSCN_SARS_RStudio_on_AnVIL Render all output courses Open Issues GitHub Branches Open PRs Website Status
jhudsl/GDSCN_Book_SARS_Galaxy_on_AnVIL Render all output courses Open Issues GitHub Branches Open PRs Website Status
jhudsl/GDSCN_Book_Statistics_for_Genomics_Differential_Expression Render all output courses Open Issues GitHub Branches Open PRs Website Status
jhudsl/GDSCN_Book_Statistics_for_Genomics_PCA Render all output courses Open Issues GitHub Branches Open PRs Website Status
jhudsl/GDSCN_Book_Statistics_for_Genomics_RNA-seq Render all output courses Open Issues GitHub Branches Open PRs Website Status
jhudsl/GDSCN_Book_Statistics_for_Genomics_scRNA-seq Render all output courses Open Issues GitHub Branches Open PRs Website Status
jhudsl/GDSCN_Book_swirl Render all output courses Open Issues GitHub Branches Open PRs Website Status
jhudsl/AnVIL_Template_Test Render all output courses Open Issues GitHub Branches Open PRs Website Status
jhudsl/GDSCN_Template_Test Render all output courses Open Issues GitHub Branches Open PRs Website Status
jhudsl/AnVIL_CoFests_2024 Render all output courses Open Issues GitHub Branches Open PRs Website Status

All illustrations CC-BY.
All other materials CC-BY unless noted otherwise.