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jykr committed Jun 21, 2024
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Expand Up @@ -187,8 +187,7 @@ resulting coefficients :math:`a = 0.2513` and :math:`b = \ - 1.9458`
are used for the analyses presented in this paper. The residual of the
regression is fitted as the Normal distribution, which is used as the
prior for the logit-scale deviation :math:`l_{\pi}` (see full detail in
`Accessibility
scaling <#adjusting-editing-rates-by-accessibility-with---scale-by-acc>`__
`Accessibility scaling <#adjusting-editing-rates-by-accessibility-with---scale-by-acc>`__
section).

``bean run`` without reporter
Expand Down Expand Up @@ -371,8 +370,11 @@ are reported. The model, variational distribution and inference
procedure are available as the default options of ``bean-run`` command
of *bean*\ :sup:`21` software. Specifically, BEAN-Uniform is run with
``--uniform-edit`` and full BEAN model is run by specifying
``--scale-by-acc`` argument. ## Adjusting editing rates by accessibility
with ``--scale-by-acc``
``--scale-by-acc`` argument.


Adjusting editing rates by accessibility with ``--scale-by-acc``
----------------------------------------------------------------------------

BEAN takes account for the observation that endogenous editing rate
 :math:`\widetilde{\mathbf{\pi}}` is roughly proportional to the
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