ReStructured Text Examples¶
Check the code (.rst) source to see how these examples are written in restructured text.
Writing your documentation using sample data¶
Where possible, you want write documentation instructions to be general enough for users can follow along with their own data. To help do this, you can use the sample data admonition to intersperse sample data-specific instructions into your generic instructions.
To do this, start your documentation with a description and where possible, a citation of the data:
How to use provided sample data
In this guide, we will use an RNA-Seq dataset (“Zika infected hNPCs”). This experiment compared human neuroprogenetor cells (hNPCs) infected with the Zika virus to non-infected hNPCs. You can read more about the experimental conditions and methods here. Where appropriate, a note (in this orange colored background) in the instructions will indicate which options to select to make use of this provided dataset.
Sample data citation: Yi L, Pimentel H, Pachter L (2017) Zika infection of neural progenitor cells perturbs transcription in neurodevelopmental pathways. PLOS ONE 12(4): e0175744. 10.1371/journal.pone.0175744
Then, as you have instructions, intersperse the sample data .. admonition
First, enter the cutoff value for your dataset
“Zika infected hNPCs” dataset:
Continue with next step…
There are several admonitions you can use, but tip and warning are the most common for our documentation.
If you don’t see a desired species/genome contact us to have it added
When naming your samples and conditions, avoid spaces and special characters (e.g. !#$%^&/, etc.). Also be sure to be consistent with spelling.
Images should only be used when necessary.
Choose an image size that works for your page:
Images should have a 1px black border: