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CHOIR improves significance-based detection of cell types and states from single-cell data
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“Unlike the density-based criterion, CHOIR does not have free parameters (for example, number of principal components, density threshold, number of nearest neighbours to consider).”
From Clonal tracing with somatic epimutations reveals dynamics of blood ageing (2025) · cites this paper as [44]
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“We used a recently published clustering method, CHOIR44, which automatically determines clusters that have statistical support in the data.”
From Clonal tracing with somatic epimutations reveals dynamics of blood ageing (2025) · cites this paper as [44]
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Performance of neural network basecalling tools for Oxford Nanopore sequencing
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Confronting false discoveries in single-cell differential expression
Squair, J. W., Gautier, M., Kathe, C., Anderson, M. A., James, N. D., Hutson, T. H., Hudelle, R., Qaiser, T., Matson, K. J. E., Barraud, Q., et al. (2021) · doi:10.1101/2021.03.12.435024 · Cited by 1,086
The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans
The Tabula Sapiens Consortium*, Jones, R. C., Karkanias, J., Krasnow, M. A., Pisco, A. O., Quake, S. R., Salzman, J., Yosef, N., Bulthaup, B., Brown, P., et al. (2022) · Science · doi:10.1126/science.abl4896 · Cited by 1,056
Orchestrating single-cell analysis with Bioconductor
Amezquita, R. A., Lun, A. T. L., Becht, E., Carey, V. J., Carpp, L. N., Geistlinger, L., Marini, F., Rue-Albrecht, K., Risso, D., Soneson, C., et al. (2020) · Nature Methods · doi:10.1038/s41592-019-0654-x · Cited by 945
Splatter: simulation of single-cell RNA sequencing data
Zappia, L., Phipson, B., & Oshlack, A. (2017) · Genome Biology · doi:10.1186/s13059-017-1305-0 · Cited by 905
FateID infers cell fate bias in multipotent progenitors from single-cell RNA-seq data
Herman, J. S., Sagar, & Grün, D. (2018) · Nature Methods · doi:10.1038/nmeth.4662 · Cited by 363
SEACells infers transcriptional and epigenomic cellular states from single-cell genomics data
Persad, S., Choo, Z.-N., Dien, C., Sohail, N., Masilionis, I., Chaligné, R., Nawy, T., Brown, C. C., Sharma, R., Pe’er, I., et al. (2023) · Nature Biotechnology · doi:10.1038/s41587-023-01716-9 · Cited by 222
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Cited by
Clonal tracing with somatic epimutations reveals dynamics of blood ageing
Scherer, M., Singh, I., Braun, M. M., Szu-Tu, C., Sanchez Sanchez, P., Lindenhofer, D., Jakobsen, N. A., Körber, V., Kardorff, M., Nitsch, L., et al. (2025) · Nature · doi:10.1038/s41586-025-09041-8 · Cited by 89
Metadata
- Authors
- Sant, C., Mucke, L., & Corces, M. R.
- Venue
- Nature Genetics
- Published
- 2025-04-07
- Volume
- 57
- Issue
- 5
- Pages
- 1309-1319
- ISSN
- 1061-4036
- 1546-1718
- PMC
- PMC12108546
- Cited by
- 18
- References
- 11
- Language
- en
- Licence
- Funders
- U.S. Department of Health & Human Services | NIH | National Institute on Aging (P01 AG073082, U01 AG072573, R21 AG085079)
- U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (UM1 HG012076)
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