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training.Rmd
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---
title: "Bioc/AnVIL training"
author: "Bioc/AnVIL team"
vignette: >
%\VignetteEngine{knitr::rmarkdown}
%\VignetteIndexEntry{training}
%\VignetteEncoding{UTF-8}
output:
BiocStyle::html_document:
highlight: pygments
number_sections: yes
theme: united
toc: yes
---
## 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](https://anvilproject.org/learn/data-analysts/using-r-bioconductor-in-anvil)
with Martin Morgan
- Week 2: [The R / Bioconductor AnVIL package](https://anvilproject.org/learn/data-analysts/the-r-bioconductor-anvil-package)
with Martin Morgan and Nitesh Turaga
- Week 3: [Running a Workflow](https://anvilproject.org/learn/data-analysts/running-a-workflow)
with Martin Morgan and Kayla Interdonato
- Week 4: [Single-cell RNASeq with 'Orchestrating Single Cell Analysis' in R / Bioconductor](https://anvilproject.org/learn/data-analysts/single-cell-rnaseq-with-orchestrating-single-cell-analysis-in-r-bioconductor) with Vince Carey
- Week 5: [Using AnVIL for Teaching R](https://anvilproject.org/learn/data-analysts/using-anvil-for-teaching-r-bioconductor)
with Levi Waldron
- Week 6: [Reproducible Research with AnVILPublish](https://anvilproject.org/learn/data-analysts/reproducible-research-with-anvilpublish)
with Martin Morgan
- Week 7: [Participant Stories](https://anvilproject.org/learn/data-analysts/participant-stories)
[Introduction to the Terra AnVIL Cloud-based Genomics Platform](https://youtu.be/N83iDYE2yQM) with
Sehyun Oh and Levi Waldron at Bioc2021
[Terra in the Classroom](https://docs.google.com/presentation/d/1AvEt6UIIx-G5eTe4hlfkGOYsUcSQrKx8ySlnnfg7XH8/edit?usp=sharing)
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](https://app.terra.bio/#workspaces/bioconductor-rpci-anvil/Bioconductor-Package-AnVIL) (public release pending)
- Simplifies exploration of the Terra data model
- Supports programmatic development of workflows, workspaces, and resource management data
-[Orchestrating Single Cell Analysis](https://app.terra.bio/#workspaces/use-strides/Bioconductor-Workshop-OSCA-3-12)
- 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](https://app.terra.bio/#workspaces/bioconductor-rpci-anvil/Bioconductor-Workflow-DESeq2)
- A collection of Jupyter notebooks
- Includes a WDL workflow that runs salmon quantification on FASTQ inputs
-[Pan-cancer Transcriptome Surveys](https://app.terra.bio/#workspaces/landmarkanvil2/pancan_tx_public) (public release pending)
- Two workflows, each devoted to different gene sets
- The WDL and scripts are registered at [dockstore.org](https://dockstore.org/workflows/github.com/vjcitn/BiocOncoTK/msireg1:master?tab=info)
- Unit testing for the script components are managed in [BiocOncoTK](https://github.com/vjcitn/BiocOncoTK/blob/master/tests/testthat/test_dockstore_scripts.R)
## Notebooks
-[Using Bioconductor's VCF processing stack](https://nbviewer.jupyter.org/github/vjcitn/terravar/blob/master/Tiny%20population%20stratification%20display.ipynb) to demonstrate population stratification using a small slice of chr17 from [EBI 1000 genomes VCF](http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/release/20190312_biallelic_SNV_and_INDEL/20190312_biallelic_SNV_and_INDEL_README.txt)
-[Using Dockstore and Terra for Pan-cancer Transcriptomics](https://nbviewer.jupyter.org/github/vjcitn/terravar/blob/master/trimmedMondaySep16.ipynb) to compare relationships between gene expression and stratified or continuous measures of microsatellite instability in 33 TCGA tumor types
## Miscellaneous
- Shiny Apps
-[TerraPlane](https://github.com/shwetagopaul92/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](resources/basicData.Rmd)
```
## # 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
```
