Code corresponding to Weinand et al., Defining optimal strategies to integrate multi-sample single-nucleus ATAC-seq datasets via a multimodal-guided approach, In Prep.
Contact: Kathryn Weinand kweinand@fas.harvard.edu
paper_figures: jupyter notebooks used to create the figures in the submitted manuscript. There is also an R file with the functions used in the jupyter notebooks. RA processed datasets from Weinand et al., Nat Comm, 2024 were obtained from Synapse syn53650034. COVID-19 processed datasets from Cheong et al., Cell, 2023 were obtained from GEO GSE196988.
scripts: The scripts used to calculate metrics. Usage information by script can be found by using Rscript {script} -h. Code snippets from our previous repo were also used to generate embeddings.