Bioc/AnVIL training

Bioc/AnVIL team

Terra / AnVIL R / Bioconductor Workshops

The following Terra / AnVIL R / Bioconductor Popup Workshops were held in 2021 from April to June.

• Week 1: Using R / Bioconductor in AnVIL with Martin Morgan
• Week 2: The R / Bioconductor AnVIL package with Martin Morgan and Nitesh Turaga
• Week 3: Running a Workflow with Martin Morgan and Kayla Interdonato
• Week 4: Single-cell RNASeq with ‘Orchestrating Single Cell Analysis’ in R / Bioconductor with Vince Carey
• Week 5: Using AnVIL for Teaching R with Levi Waldron
• Week 6: Reproducible Research with AnVILPublish with Martin Morgan
• Week 7: Participant Stories

Introduction to the Terra AnVIL Cloud-based Genomics Platform with Sehyun Oh and Levi Waldron at Bioc2021

Terra in the Classroom documents the experience of running a small course utilizing AnVIL. Includes some set up, learned positives and negatives from February 2020.

Workspaces

See illustrative examples of how you can use Bioconductor in AnVIL workspaces.

• The AnVIL package (public release pending)
  • Simplifies exploration of the Terra data model
  • Supports programmatic development of workflows, workspaces, and resource management data
• Orchestrating Single Cell Analysis
  • Describes how to use a custom container to do all computations in the OSCA book [current to March 2021]
  • Note: another workspace processes the book content via AnVILPublish
• RNA-seq analysis with DESeq2
  • A collection of Jupyter notebooks
  • Includes a WDL workflow that runs salmon quantification on FASTQ inputs
• Pan-cancer Transcriptome Surveys (public release pending)
  • Two workflows, each devoted to different gene sets
  • The WDL and scripts are registered at dockstore.org
  • Unit testing for the script components are managed in BiocOncoTK

Notebooks

• Using Bioconductor’s VCF processing stack to demonstrate population stratification using a small slice of chr17 from EBI 1000 genomes VCF
• Using Dockstore and Terra for Pan-cancer Transcriptomics to compare relationships between gene expression and stratified or continuous measures of microsatellite instability in 33 TCGA tumor types

Miscellaneous

• Shiny Apps

  • TerraPlane filters Dockstore to find methods based on search terms

• Data Management Utilities

  • Results as of 20 June 2019

    • R markdown for using terra to survey CCDG and CM

  ## # A tibble: 10 x 3
  ## # Groups:   study [2]
  ##    study organ      N
  ##    <chr> <chr>  <int>
  ##  1 CCDG  AI      9031
  ##  2 CCDG  CVD    25741
  ##  3 CCDG  NP     19422
  ##  4 CMG   Blood    277
  ##  5 CMG   Brain   1844
  ##  6 CMG   Eye      552
  ##  7 CMG   Heart    184
  ##  8 CMG   Kidney   432
  ##  9 CMG   Muscle  1722
  ## 10 CMG   Orphan   717

  • Drilling down on CCDG

  ## # A tibble: 9 x 4
  ## # Groups:   study, organ [3]
  ##   study organ addit         N
  ##   <chr> <chr> <chr>     <int>
  ## 1 CCDG  AI    Asthma     1171
  ## 2 CCDG  AI    IBD        4694
  ## 3 CCDG  AI    T1D        3166
  ## 4 CCDG  CVD   AFib       3731
  ## 5 CCDG  CVD   EOCAD     20156
  ## 6 CCDG  CVD   HemStroke  1358
  ## 7 CCDG  CVD   Stroke      496
  ## 8 CCDG  NP    Alz        2374
  ## 9 CCDG  NP    Autism    17048