.. |counts_in_region| replace:: :py:mod:`~plastid.bin.counts_in_region`
.. |crossmap| replace:: :py:mod:`~plastid.bin.crossmap`
.. |cs| replace:: :py:mod:`~plastid.bin.cs`
.. |demux_reads| replace:: :py:mod:`~plastid.bin.demux_reads`
.. |findjuncs| replace:: :py:mod:`~plastid.bin.findjuncs`
.. |get_count_vectors| replace:: :py:mod:`~plastid.bin.get_count_vectors`
.. |gff_parent_types| replace:: :py:mod:`~plastid.bin.gff_parent_types`
.. |make_wiggle| replace:: :py:mod:`~plastid.bin.make_wiggle`
.. |metagene| replace:: :py:mod:`~plastid.bin.metagene`
.. |phase_by_size| replace:: :py:mod:`~plastid.bin.phase_by_size`
.. |psite| replace:: :py:mod:`~plastid.bin.psite`
.. |reformat_transcripts| replace:: :py:mod:`~plastid.bin.reformat_transcripts`
.. |slidejuncs| replace:: :py:mod:`~plastid.bin.slidejuncs`

.. |bin| replace:: :py:obj:`plastid.bin`
.. |genomics| replace:: :py:obj:`plastid.genomics`
.. |readers| replace:: :py:obj:`plastid.readers`
.. |plotting| replace:: :py:obj:`plastid.plotting`
.. |scriptlib| replace:: :py:obj:`plastid.util.scriptlib`
.. |util| replace:: :py:obj:`plastid.util`
.. |test| replace:: :py:obj:`plastid.test`
