The manifesto, workshops and tutorials of the tidy transcriptomics. All this is very work-in-progress

This document lays down the principles of tidy transcriptomics, of which tidybulk and tidysc are based on. These principles are in line with the tidy tools manifesto.

• Use easy-to-understand, verbose, jargon- and acronym-free vocabulary. If the English dictionary is not enough to understand the underlying meaning of a function or a variable name, it is a bad sign. Learning is incredibly slown-down by a cryptic vocabulary; and the cost of saving few characters is usually bigger than you think.
• Present/visualise information in its raw form when possible. Modern visualisation tools (e.g. ggplot) allow to use custom scales to visualise data. For example, for visualising p-values apply the log10_reverse scale instead of transforming the p-values in their negative-log form; for visualising (raw, scaled and/or adjusted) transcript abundance (in the form of read counts) use the log1p scale instead of transforming the data in its log (or count-per-million) form.
• Avoid the creation of temporary variables when possible, and always avoid variable updating. When working interactively, data-containing variables is a bug-prone process, especially if multiple assignments are done on the same variable though the workflow. The main utility of variables should be to store data that is used more than once. Tidyverse allows extremely complex operations in a functional way.

Workshops

30 minutes

• Converion SummarizedExperiment object to tibble
• Format sample column
• Get gene symbol
• Identify abundant transcripts
• Scale abundance for sequencing depth
• Visualise abundance distribution
• Reduce dimensions
• Draw heatmap
• Test differential transcript abundance
• Volcano plot
• Strip-chart
• Interactive plots

1h

• Import tibble
• comparison of different differential transcript abundance testing tools
• Strip-chart comparing all normalisations of top genes
• Gene enrichment analyses

2h

• signature creation
• single cell sudobulk
• nest functionality

Via GitHub

Alternatively, you could install the workshop using the commands below in R 4.0.

devtools::install_github("stemangiola/tidybulk")
devtools::install_github("stemangiola/tidytranscriptomics", build_vignettes = TRUE)
library(tidytranscriptomics)
vignette("tidytranscriptomics")