The universe was initially filled with dust, which had almost uniform density but there were some places where just a little bit higher than elsewhere (around one part in 100000). Gravity started to accrete dust to these places, the density would grow there and therefore more galaxies would form there. These became clusters (or clumps) of galaxies. If you think of the initial random densities, you note that the minima are connected to each other by “ridges” where the density is lower than at the maximum but still higher than elsewhere. Gravity squeezes these ridges into filaments.
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