This tutorial will showcase analysis of single-cell RNA sequencing data following the tidy data paradigm. The tidy data paradigm provides a standard way to organise data values within a dataset, where each variable is a column, each observation is a row, and data is manipulated using an easy-to-understand vocabulary. Most importantly, the data structure remains consistent across manipulation and analysis functions.
This can be achieved with the integration of packages present in the R CRAN and Bioconductor ecosystem, including tidySingleCellExperiment and tidyverse. These packages are part of the tidytranscriptomics suite that introduces a tidy approach to RNA sequencing data representation and analysis. For more information see the tidy transcriptomics blog.
Material web page. More details on the workshop are below.
For the BioC2022 workshop, an RStudio in the cloud will be provided with everything installed, all that participants will need is a web browser.
If you want to install the packages and material post-workshop, they can be installed using one of the two ways below. The workshop is designed for R
4.2 and Bioconductor 3.16.
If you’re familiar with Docker you could use the Docker image which has all the software pre-configured to the correct versions.
docker run -e PASSWORD=abc -p 8787:8787 ghcr.io/tidytranscriptomics-workshops/bioc2022_tidytranscriptomics
Once running, navigate to http://localhost:8787/ and then login with
You should see the Rmarkdown file with all the workshop code which you can run.
Alternatively, you could install the workshop using the commands below in R
#install.packages('remotes') # Need to set this to prevent installation erroring due to even tiny warnings, similar to here: https://github.com/r-lib/remotes/issues/403#issuecomment-748181946 Sys.setenv("R_REMOTES_NO_ERRORS_FROM_WARNINGS" = "true") # Install same versions used in the workshop remotes::install_github(c("stemangiola/tidySingleCellExperiment@v1.7.4", "stemangiola/tidySummarizedExperiment@v1.7.3", "firstname.lastname@example.org")) # Install workshop package remotes::install_github("tidytranscriptomics-workshops/bioc2022_tidytranscriptomics", build_vignettes = TRUE) # To view vignettes library(bioc2022tidytranscriptomics) browseVignettes("bioc2022tidytranscriptomics")
To run the code, you could then copy and paste the code from the workshop vignette or R markdown file into a new R Markdown file on your computer.