Data Analysts - Guides and Tutorials

Bioconductor / RStudio

• Getting Started with Bioconductor - Guides helping R / Bioconductor users start RStudio or Jupyter for interactive analysis and workflows for large-scale data processing.
• Starting RStudio on the AnVIL Platform - A video introduction to using RStudio on the AnVIL platform.

2021 Bioconductor Popup Workshops

Recordings and related materials for the 2021 Bioconductor popup workshops are listed below:

• Week 1: Using R / Bioconductor in AnVIL - An introduction to the AnVIL cloud computing environment. We learn how to create a Google account to use in AnVIL. We explore key concepts related to workspaces and billing projects. We explore creating a Jupyter notebooks-based cloud environment, and an RStudio cloud environment.
• Week 2: The R / Bioconductor AnVIL Package - An exploration of how workspaces provide a framework for managing data and large-scale analyses using the HCA Optimus Pipeline and 1000G-high-coverage-2019 workspaces and R using the AnVIL package.
• Week 3: Running a Workflow - How to configure and run a workflow, based on the Bioconductor-Workflow-DESeq2 workspace. The workflow starts with FASTQ files and transforms them using salmon to the inputs required for Bioconductor DESeq2 analysis of differential expression.
• Week 4: Single-cell RNASeq with 'Orchestrating Single Cell Analysis' in R / Bioconductor - An introduction to a resource, developed primarily by Aaron Lun of Genentech, Inc., that employs Bioconductor resources for many aspects of the analysis of single-cell RNA-seq data. The resource is a "computable book" written in R Markdown, published at https://bioconductor.org/books/release/OSCA.
• Week 5: Using AnVIL for Teaching R - A case study of using AnVIL to teach R for a Biostatistics course and provides essentials for using AnVIL for other instructional efforts.
• Week 6: Reproducible Research with AnVILPublish - An exploration of elements of reproducible research with the AnVILPublish package. We will illustrate how to make a docker container tailored publishing AnVIL packages and then emphasize the merits of an R package structure for organizing research activities in a manner that emphasizes provenance and reproducibility.
• Week 7: Participant Stories - Participants share their own use of AnVIL.

Galaxy

• Getting Started with Galaxy - A step-by-step tutorial demonstrating how to compute quality metrics of unaligned reads, align the reads to a reference genome using bowtie2, plot a coverage histogram, call variants using FreeBayes, and then summarize the variant calls using bcftools.
• Starting Galaxy on the AnVIL Platform - A video introduction to using Galaxy on the AnVIL platform.

Jupyter

• Starting Jupyter on the AnVIL Platform - A video introduction to using Jupyter Notebooks on the AnVIL platform.