This repository contains the code that was used for creating the code in the manuscript. For the actual software package see our Cobolt github repos.

The PBMC datasets were downloaded from the 10X website:

• Multiome Chromium X: https://support.10xgenomics.com/single-cell-multiome-atac-gex/datasets/2.0.0/10k_PBMC_Multiome_nextgem_Chromium_X
• Multiome unsorted: https://www.10xgenomics.com/resources/datasets/pbmc-from-a-healthy-donor-no-cell-sorting-10-k-1-standard-2-0-0
• scRNA-seq:https://www.10xgenomics.com/resources/datasets/20-k-human-pbm-cs-3-ht-v-3-1-chromium-x-3-1-high-6-1-0
• scATAC-seq: https://support.10xgenomics.com/single-cell-atac/datasets/2.0.0/10k_PBMC_ATAC_nextgem_Chromium_X