This repository contains code used in the analysis of the manuscript: "Developmental and evolutionary dynamics of cis-regulatory elements in mouse cerebellar cells" https://doi.org/10.1126/science.abg4696. This is the peer-reviewed version of the preprint "The regulatory landscape of cells in the developing mouse cerebellum" https://doi.org/10.1101/2021.01.29.428632.

Some analyses have been updated as part of the peer review process. You can still access the original code used for the biorxiv version in the branch "biorxiv_v1". However, we highly recommend using the updated scripts as these contain substantial updates compared to the original version.

A few terms have been renamed in the final preparation of the manuscript (ms):

1. The progenitor type referred to as "Uncommitted" in the ms is described as "Progenitor" in the scripts.
2. "Vascular" cells in the ms are described as "Mural/endothelia" in the scripts.
3. Embryonic stages are capitalised in the ms. Lowercase is used in the scripts (i.e., e13=E13). Also P04=P4.
4. GABAergic interneurons are spelled out as "Interneuron" in the scripts, but abbreviated as "IN" in the ms.
5. Progenitor subtypes are typically designated by a "Progenitor_" prefix in the scripts but not in the ms (i.e. Progenitor_bipotent = Bipotent).
6. In the ms we collectively refer to intergenic and intronic CREs as "distal". In the scripts we follow ArchR's terminology, where distal is used for intergenic CREs.