SPECK: Receptor Abundance Estimation using Reduced Rank Reconstruction and Clustered Thresholding (original) (raw)
Surface Protein abundance Estimation using CKmeans-based clustered thresholding ('SPECK') is an unsupervised learning-based method that performs receptor abundance estimation for single cell RNA-sequencing data based on reduced rank reconstruction (RRR) and a clustered thresholding mechanism. Seurat's normalization method is described in: Hao et al., (2021) <doi:10.1016/j.cell.2021.04.048>, Stuart et al., (2019) <doi:10.1016/j.cell.2019.05.031>, Butler et al., (2018) <doi:10.1038/nbt.4096> and Satija et al., (2015) <doi:10.1038/nbt.3192>. Method for the RRR is further detailed in: Erichson et al., (2019) <doi:10.18637/jss.v089.i11> and Halko et al., (2009) <doi:10.48550/arXiv.0909.4061>. Clustering method is outlined in: Song et al., (2020) <doi:10.1093/bioinformatics/btaa613> and Wang et al., (2011) <doi:10.32614/RJ-2011-015>.
Version: | 1.0.0 |
---|---|
Depends: | R (≥ 2.10) |
Imports: | Ckmeans.1d.dp, magrittr, Matrix (≥ 1.6.1.1), rsvd, Seurat |
Suggests: | ggplot2, gridExtra, knitr, rmarkdown, SeuratObject, usethis |
Published: | 2023-11-17 |
DOI: | 10.32614/CRAN.package.SPECK |
Author: | H. Robert Frost [aut], Azka Javaid [aut, cre] |
Maintainer: | Azka Javaid <azka.javaid.gr at dartmouth.edu> |
License: | GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
NeedsCompilation: | no |
CRAN checks: | SPECK results |
Documentation:
Downloads:
Reverse dependencies:
Linking:
Please use the canonical formhttps://CRAN.R-project.org/package=SPECKto link to this page.