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* Complete reimplementation of RnaChipIntegrator to unify internal
algorithms, simplify usage and substantially update the
documentation.
* Installs using ``pip``; can be obtained directly from PyPI using
``pip install RnaChipIntegrator``.
* Executable now installs as ``RnaChipIntegrator`` (i.e. no ``.py``
extension)
* Documentation now available via ReadTheDocs:
http://rnachipintegrator.readthedocs.org/en/latest/
* No distinction is now made between 'summits' and 'peaks'; the
same algorithm is applied in each case.
* The program always finds the nearest genes to each peak, and
vice versa. The same distance cutoff and maximum number of hits
are applied to both and can be specified using the ``--cutoff``
and ``--number`` options.
* By default all pairs within the cut-off distance are reported
unless the user explicitly restricts this to a subset by
specifying the ``--number`` option (i.e. ``--number`` now turned
off by default).
* By default nearest distances between peaks and gene are
calculated from the TSS of the feature to whichever of the peak
edges are closer; alternatively distances can be calculated
between the nearest pair of peak/gene edges by specifying the
``--edge=both`` option.
* Any differential expression flags in the input genes file
are ignored unless the ``--only-DE`` option is specified, in which
case only the differentially expressed genes are considered
in the analyses.
* By default each peak/gene pair is reported on a separate
line; the ``--compact`` option reports all nearest gene/peaks
on a single line of output.
* New ``direction`` field in output indicates whether hits are
up- or downstream from reference.
* Specify arbitrary columns from input peaks file using new
``--peak_cols`` options to set chromosome, start and end.
* Output file names now end with ``gene-centric`` and
``peak-centric``.
* Excel output is only produced if the ``--xlsx`` option is
specified; spreadsheets are now output in XLSX format (instead
of XLS).
* Summary output is only produced if ``--summary`` is specified.
* The ``rearrange_columns.py`` utility has been dropped.
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