.. _notebooks:

Notebooks
=========

Runnable Jupyter notebooks that walk through the Python API. They are
rendered as static HTML here; click any notebook to download or run it
yourself.

.. toctree::
   :maxdepth: 1

   notebooks/BAM
   notebooks/coverage
   notebooks/fastq_module
   notebooks/featurecounts
   notebooks/ribodesigner

Notebook map
------------

``BAM.ipynb``
    Read a BAM file, compute alignment statistics, plot insert size.
``coverage.ipynb``
    Companion to :ref:`userguide` — running median + z-score on a BED.
``fastq_module.ipynb``
    Iterate over FastQ records, filter and re-write.
``featurecounts.ipynb``
    Load a featureCounts table, inspect the count matrix.
``ribodesigner.ipynb``
    Design ribosomal-depletion probes from a FASTA + GFF.