SPECK: Receptor Abundance Estimation using Reduced Rank Reconstructionand Clustered Thresholding
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: | 1.0.1 |
| Depends: | R (≥ 3.5) |
| Imports: | Ckmeans.1d.dp,magrittr,Matrix (≥ 1.6.1.1),rsvd,Seurat |
| Suggests: | ggplot2,gridExtra,knitr,rmarkdown,SeuratObject,usethis |
| Published: | 2025-10-05 |
| 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.