cellID-package: Multiple Correspondence Analysis on Single Cell for Joint...

In RausellLab/CelliD: Unbiased Extraction of Single Cell gene signatures using Multiple Correspondence Analysis

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 [e-mail]

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

RausellLab/CelliD documentation built on Jan. 12, 2024, 3:44 a.m.