Single-cell methods have proven to be a powerful tool in the interrogation of complex biology. One such biological system in which single-cell methods have been paramount to the discovery of complex disease and cell development is in the mammalian cortex. In this thesis I present an overview of single-cell method development for chromatin accessibility, chromatin conformation, whole genome sequencing, and whole methylome sequencing. I then proceed to describe the development and application of novel single-cell methylome methods, and apply this to a murine cortical sample to study neuronal methylomes. I present a new generalized chemistry to improve upon the established single-cell combinatorial indexing (sci) flow-through. This leads to substantial improvements of information garnered per cell for chromatin accessibility, chromatin conformation, and whole genome sequencing. I also apply a method to combine two prominent methods for single-cell chromatin accessibility to increase cellular throughput by over 15-fold. I apply this new method for a survey of murine and human mature cortex. Finally, I demonstrate the use of single-cell chromatin assays on the study of chromatin dynamics during corticogenesis in a model system of human forebrain development. Within this system, dynamic changes of enhancer usage for promoter, as well as the transcription factor usage changes as cells develop and mature into the mid-gestation cortex. This body of work bolsters the field of single-cell genomics by introducing novel strategies which address several key hurdles. Further, this work presents the generation of cell type and state atlases of human and mouse cortices.