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. 2022 Jan 12;23:20. doi: 10.1186/s13059-021-02595-6

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© The Author(s) 2022

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 2 — scMVP mitigates data sparsity in joint profiling datasets. a Correlation between original and imputed gene expression of each cell from scRNA of joint profiling datasets and gene expression in corresponding bulk RNA-seq dataset. A549 cell lines treated with DEX for 0h (ENCSR632DQP), 1h (ENCSR656FIH), 3h (ENCSR624RID) in sci-CAR dataset, HepG2 cell line (ENCSR058OSL) in Paired-seq dataset and H1 (ENCSR670WQY), BJ (ENCSR000COP), K562 (ENCSR530NHO), and GM12878 (ENCSR000CPO) cell lines in SNARE-seq dataset were used for benchmark. b Number of bulk ATAC peaks identified by raw and imputed scATAC in each cell. c Ratio of raw and imputed scATAC peaks identified in bulk ATAC peaks. DNase-seq signal files for H1 (ENCSR000EMU) and BJ (ENCSR000EME), and ATAC-seq signal files for K562 (ENCSR868FGK) and GM12878 (ENCSR095QNB) were used for benchmark