Hi all,
We have a new version of the startup script for AnVIL users! This update adds a new dataset, a new RNA-seq project module, and lays the foundation to make future updates to the script (and thus the curriculum on AnVIL) easier.
What do I have to do?
I’ve replaced the link to the startup script in all of the workspaces at our current pilot sites (CCC, NDMU, and WCC). If you are an instructor or a student in one of these classes, please make sure you use the new version of the startup script! For example, if you copied the old startup script to a word document to reference, make sure you don’t enter the old script.
What’s new?: Mouse brain dataset
This update includes an additional new dataset based on a subset of data from the Sharon et al. study, Human Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice.
Although drastically different in overall shape and size, the human and mouse brain are remarkably similar in structure and organization and show homology in neural pathways. Specific parts of the brain are known to be responsible for a specific function, such as the amygdala which control emotions. This dataset provides an opportunity to explore gene-expression in two areas of the brain responsible for social behavior, the Prefrontal cortex (PFC) and the Striatum (STR). These two brain sections are in close proximity to each other and are hypothesized to have similar functions, though each region’s exact purpose and their relationship to each other are still being studied.
To access this dataset, go to the new RNA-seq project work module. In the RStudio file explorer:
- Click on the rnaseq folder to enter it
- Click on the 10-rnaseq-proj folder to enter it
- Click on the rna-seq-project-work.Rmd to open the file
- Click on “Run Document” in the top left section of the screen that opens (not “Run”)
What’s in the script?
The raw link to the script is here:
This is awesome!