The DOI matches its Crossref record; 55 of the 55 references it cites were found in a registry or an index.
Single-cell mRNA quantification and differential analysis with Census
Open accessAbstract
Single-cell gene expression studies promise to reveal rare cell types and cryptic states, but the high variability of single-cell RNA-seq measurements frustrates efforts to assay transcriptional differences between cells. We introduce the Census algorithm to convert relative RNA-seq expression levels into relative transcript counts without the need for experimental spike-in controls. Analyzing changes in relative transcript counts led to dramatic improvements in accuracy compared to normalized read counts and enabled new statistical tests for identifying developmentally regulated genes. Census counts can be analyzed with widely used regression techniques to reveal changes in cell-fate-dependent gene expression, splicing patterns and allelic imbalances. We reanalyzed single-cell data from several developmental and disease studies, and demonstrate that Census enabled robust analysis at multiple layers of gene regulation. Census is freely available through our updated single-cell analysis toolkit, Monocle 2.
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Cites
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Cited by
Scenic: single-cell regulatory network inference and clustering.
Aibar, S., González-Blas, C. B., Moerman, T., Huynh-Thu, V. A., Imrichova, H., Hulselmans, G., Rambow, F., Marine, J.-C., Geurts, P., Aerts, J., et al. (2017) · Nature Methods · doi:10.1038/nmeth.4463 · Cited by 6,520
Reversed graph embedding resolves complex single-cell trajectories
Qiu, X., Mao, Q., Tang, Y., Wang, L., Chawla, R., Pliner, H. A., & Trapnell, C. (2017) · Nature Methods · doi:10.1038/nmeth.4402 · Cited by 5,070
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MethodSlingshot: cell lineage and pseudotime inference for single-cell transcriptomics
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Deep generative modeling for single-cell transcriptomics
Lopez, R., Regier, J., Cole, M. B., Jordan, M. I., & Yosef, N. (2018) · Nature Methods · doi:10.1038/s41592-018-0229-2 · Cited by 2,530
Metadata
- Authors
- Qiu, X., Hill, A., Packer, J., Lin, D., Ma, Y.-A., & Trapnell, C.
- Venue
- Nature Methods
- Published
- 2017-01-23
- Volume
- 14
- Issue
- 3
- Pages
- 309-315
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- OpenAlex
- W2582033455
- Cited by
- 1,918
- References
- 55
- FWCI
- 38.92
- Type
- journal article
- Language
- en
- Open access
- green
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