Facilitating single-cell chromatin accessibility research with a user-friendly database

References

[1] Chen X, Chen S, Song S, Gao Z, Hou L, Zhang X, Lv H, Jiang R . Cell type annotation of single-cell chromatin accessibility data via supervised Bayesian embedding. Nature Machine Intelligence, 2022, 4( 2): 116–126

[2] Buenrostro J D, Wu B, Litzenburger U M, Ruff D, Gonzales M L, Snyder M P, Chang H Y, Greenleaf W J . Single-cell chromatin accessibility reveals principles of regulatory variation. Nature, 2015, 523( 7561): 486–490

[3] Danese A, Richter M L, Chaichoompu K, Fischer D S, Theis F J, Colomé-Tatché M . EpiScanpy: integrated single-cell epigenomic analysis. Nature Communications, 2021, 12( 1): 5228

[4] Fang R, Preissl S, Li Y, Hou X, Lucero J, Wang X, Motamedi A, Shiau A K, Zhou X, Xie F, Mukamel E A, Zhang K, Zhang Y, Behrens M M, Ecker J R, Ren B . Comprehensive analysis of single cell ATAC-seq data with SnapATAC. Nature Communications, 2021, 12( 1): 1337

[5] Stuart T, Srivastava A, Madad S, Lareau C A, Satija R . Single-cell chromatin state analysis with Signac. Nature Methods, 2021, 18( 11): 1333–1341

[6] Granja J M, Corces M R, Pierce S E, Bagdatli S T, Choudhry H, Chang H Y, Greenleaf W J . ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis. Nature Genetics, 2021, 53( 3): 403–411

[7] Wolf F A, Angerer P, Theis F J . SCANPY: large-scale single-cell gene expression data analysis. Genome Biology, 2018, 19( 1): 15

[8] Feng S, Li S, Chen L, Chen S . Unveiling potential threats: backdoor attacks in single-cell pre-trained models. Cell Discovery, 2024, 10( 1): 122

[9] Chen S, Yan G, Zhang W, Li J, Jiang R, Lin Z . RA3 is a reference-guided approach for epigenetic characterization of single cells. Nature Communications, 2021, 12( 1): 2177

[10] Li S, Zhuang X, Jia S, Tang S, Yan L, Hua H, Jia Y, Zhang X, Zhang Y, Yang Q, Chen S. MultiKano: an automatic cell type annotation tool for single-cell multi-omics data based on Kolmogorov-Arnold network and data augmentation. Protein & Cell, 2024

[11] Tang S, Cui X, Wang R, Li S, Li S, Huang X, Chen S . scCASE: accurate and interpretable enhancement for single-cell chromatin accessibility sequencing data. Nature Communications, 2024, 15( 1): 1629

RIGHTS & PERMISSIONS

Higher Education Press