OSTA Workshop Bioc2021

This repository contains materials for our OSTA workshop at the Bioc2021 conference.

Links

• Workshop website: https://lmweber.org/OSTAWorkshopBioc2021/
• Workshop source repository: https://github.com/lmweber/OSTAWorkshopBioc2021
• OSTA website: https://lmweber.org/OSTA-book/
• OSTA source repository: https://github.com/lmweber/OSTA-book

Overview

Our online textbook Orchestrating Spatially Resolved Transcriptomics Analysis with Bioconductor (OSTA) describes the steps in a computational analysis pipeline for spatially resolved transcriptomics (ST) data using the Bioconductor framework in R, including examples and workflows with R code and datasets.

OSTA is built around the SpatialExperiment object class and the Bioconductor principle of modularity, which allows users to easily adapt the pipeline to substitute alternative or updated methods for individual steps.

In particular, OSTA and SpatialExperiment are compatible with SingleCellExperiment, allowing existing methods and pipelines developed for single-cell RNA sequencing data (such as those described in OSCA) to be re-used and adapted to the spatial context.

Prerequisites

• Intermediate level of R programming
• Basic familiarity with Bioconductor object classes, e.g. SpatialExperiment and/or SingleCellExperiment
• Basic knowledge of spatially resolved transcriptomics (ST) technologies

Installation

For this workshop, we will use R version 4.1 and a devel installation of Bioconductor 3.14. In addition, you will need to install the following package from GitHub:

remotes::install_github("lmweber/ggspavis", build_vignettes = TRUE)

Alternatively, you can use a release version of Bioconductor 3.13 along with the following versions of packages installed from GitHub:

remotes::install_github("drighelli/SpatialExperiment", build_vignettes = TRUE)
remotes::install_github("lmweber/STexampleData", ref = "no_accessors", build_vignettes = TRUE)
remotes::install_github("lmweber/ggspavis", build_vignettes = TRUE)

Docker image

A Docker image containing a complete version of all materials used in the workshop is also available. Note this is a large download.

To run the Docker image:

docker run -e PASSWORD=abc -p 8787:8787 lmweber/ostaworkshopbioc2021:latest

Then navigate to http://localhost:8787/ in your browser, and log in with username rstudio and password abc.

Acknowledgments

OSTA contributors:

• Abby Spangler, Lieber Institute for Brain Development, Baltimore, MD, USA
• Madhavi Tippani, Lieber Institute for Brain Development, Baltimore, MD, USA
• Leonardo Collado-Torres, Lieber Institute for Brain Development, Baltimore, MD, USA
• Stephanie C. Hicks, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA

SpatialExperiment:

• Dario Righelli, Department of Statistical Sciences, University of Padova, Padova, Italy
• Helena L. Crowell, Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
• Aaron Lun, Genentech, South San Francisco, CA, USA
• Stephanie C. Hicks, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
• Davide Risso, Department of Statistical Sciences, University of Padova, Padova, Italy