Bioc/AnVIL training

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