  We investigate Lyman-alpha (Ly$\alpha$) transmission spikes at $5.2 < z <
6.8$ using synthetic quasar spectra from the ``Cosmic Reionization On
Computers" simulations. We focus on understanding the relationship between
these spikes and the properties of the intergalactic medium (IGM).
Disentangling the complex interplay between IGM physics and the influence of
galaxies on the generation of these spikes presents a significant challenge. To
address this, we employ Explainable Boosting Machines, an interpretable machine
learning algorithm, to quantify the relative impact of various IGM properties
on the Ly$\alpha$ flux. Our findings reveal that gas density is the primary
factor influencing absorption strength, followed by the intensity of background
radiation and the temperature of the IGM. Ionizing radiation from local sources
(i.e. galaxies) appears to have a minimal effect on Ly$\alpha$ flux. The
simulations show that transmission spikes predominantly occur in regions of low
gas density. Our results challenge recent observational studies suggesting the
origin of these spikes in regions with enhanced radiation. We demonstrate that
Ly$\alpha$ transmission spikes are largely a product of the large-scale
structure, of which galaxies are biased tracers.
