Source code

The notebooks and other source code are available on GitHub. This includes the pre-processing pipelines and data files required to reproduce the RNA-seq and insertion analyses.

The repository has the following structure:

├── environment.yml    <- File describing the conda environment.
├── LICENSE
├── Makefile           <- Makefile with commands.
├── README.md          <- The top-level README for developers using this project.
│
├── configs            <- Configs for the Snakemake pipelines.
│
├── data
│   ├── external       <- Data from third party sources.
│   ├── interim        <- Intermediate data that has been transformed.
│   ├── processed      <- The final, canonical data sets for the analyses.
│   └── raw            <- The original, immutable data dump.
│
├── docs               <- Source for this documentation.
│
├── notebooks          <- Jupyter notebooks.
│
├── pipelines          <- Snakemake pipeline definitions.
│
├── references         <- Data dictionaries, manuals, and all other explanatory materials.
│
├── reports            <- Generated analysis as HTML, PDF, LaTeX, etc.
│   │── figures        <- Main figure panels.
│   │── supplemental   <- Supplemental figures/tables.
│   └── tables         <- Main tables.
│
└── src                <- Source code for use in this project.
   └── nbsupport       <- Module containing notebook supporting code.

The main analyses are described in the Jupyter notebooks. Supporting code is provided in the nbsupport module under the src directory. Figures/Tables generated by the notebooks are stored in the appropriate location under the reports directory.