This Zenodo record contains the custom analysis code associated with the manuscript entitled “Comprehensive profiling of CRISPR/dCas9 epigenome editors indicates a complex link between on and off target effects”. The archived materials comprise the scripts and computational workflows used to process and analyze EPIC DNA methylation array data, targeted methyl sequencing (TMS), and RNA-sequencing datasets generated in the study. All analysis pipelines are publicly maintained in the following GitLab repository:https://gitlab.com/jagodiclab/epigenomeediting The code archived here corresponds to the version used for the analyses reported in the manuscript and is deposited on Zenodo to ensure long-term accessibility and to provide a persistent, citable DOI. The sequencing datasets analyzed using these pipelines are publicly available in the Gene Expression Omnibus (GEO) under the following accession numbers: GSE297385 (EPIC) GSE297389 (TMS1_day3) GSE297430 (RNAseq1_day3) GSE297432 (TMS2_days3, 7, 14, 21, 30) GSE297435 (RNAseq2_days3, 7, 30)