CelliD-package {CelliD} | R Documentation

## Multiple Correspondence Analysis on Single Cell for Joint Dimensionality Reduction of Gene and Cell, Cells Geneset Extraction and Geneset Enrichment Analysis

### Description

CelliD is a clustering-free multivariate statistical method for the robust extraction of per-cell gene signatures from single-cell RNA-seq. CelliD allows unbiased cell identity recognition across different donors, tissues-of-origin, model organisms and single-cell omics protocols. The package can also be used to explore functional pathways enrichment in single cell data.

### Author(s)

Maintainer: Akira Cortal akira.cortal@institutimagine.org

Authors:

- Akira Cortal

- Antonio Rausell

### References

- Rausell, A., Juan, D., Pazos, F., & Valencia, A. (2010). Protein interactions and ligand binding: from protein subfamilies to functional specificity. Proceedings of the National Academy of Sciences of the United States of America, 107(5), 1995–2000. https://doi.org/10.1073/pnas.0908044107

- Aan, Z., & Greenacre, M. (2011). Biplots of fuzzy coded data. Fuzzy Sets and Systems, 183(1), 57–71. https://doi.org/10.1016/j.fss.2011.03.007

- Alexey Sergushichev. An algorithm for fast preranked gene set enrichment analysis using cumulative statistic calculation. bioRxiv (2016), https://doi.org/10.1101/060012

- Stuart and Butler et al. Comprehensive integration of single cell data. bioRxiv (2018). https://doi.org/10.1101/460147

- Aaron Lun and Davide Risso (2019). SingleCellExperiment: S4 Classes for Single Cell Data. R package version 1.4.1.

### See Also

- McCarthy, D. J., Campbell, K. R., Lun, A. T. L., & Wills, Q. F. (2017). Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R. Bioinformatics, 33(8), btw777. https://doi.org/10.1093/bioinformatics/btw777

- Amezquita, R. A., Carey, V. J., Carpp, L. N., Geistlinger, L., Lun, A. T. L., Marini, F., … Hicks, S. C. (2019). Orchestrating Single-Cell Analysis with Bioconductor. BioRxiv, 590562. https://doi.org/10.1101/590562

[Package CelliD version 1.2.1 Index]