This repository contains the processed data and Jupyter notebooks used in the creation of figures for the RNAvigate manuscript.
There are three options to view these notebooks:
- Static notebooks: loads instantly, no installation required
- Interactive notebooks via Binder: loads quickly (see disclaimer), no installation required
- Interactive notebooks via local installation
View the notebooks as static HTML web pages in your browser.
figure 1, figure 2, figure 3, figure 4, figure 5, figure 6
Use Binder, a free web service from Project Jupyter, to run the notebooks in a cloud computing environment.
- Click on the link above.
Usually, Binder will start up quickly, within a minute. Binder has limited computational resources and may impose longer wait times. In my experience, if it takes more than 10 minutes, it is best to try again later. Once the cloud environment is ready, Jupyter Lab will open in your browser.
- Navigate to and open an interactive notebook using the left-hand panel (locations below).
interactive_notebooks/
├── figure_1/
| └── F1_simple_plots.ipynb
├── figure_2/
| └── F2_smCCP_tmRNA.ipynb
├── figure_3/
| └── F3_lowSS_DENV.ipynb
├── figure_4/
| └── F4_tr-folding_RNaseP.ipynb
├── figure_5/
| └── F5_DANCE_add-riboswitch.ipynb
└── figure_6/
└── F6_compare_SARS2.ipynb
- Hit the double-play button in the top ribbon (restart and run all cells).
The code will run, and figures from the manuscript will be recreated. Most figures are generated within seconds; some, especially kernel density estimates, may take a minute.
If a warning appear, but does not prevent the notebook from executing, it can be safely ignored. If anything prevents the notebooks from executing, please submit a GitHub issue.
Download this repository (RNAvigate_figures). In order to run the Jupyter notebooks, you will need a working RNAvigate installation:
In future versions of RNAvigate, syntax changes may prevent these notebooks from running properly. If that is the case, here is the hard link to the version of RNAvigate used in these notebooks.