===========
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:

.. parsed-literal::

    ├── 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.

.. _GitHub: https://github.com/jrderuiter/ilc-sb-screen