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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 |
Reference manual: | SPECK.pdf |
Vignettes: |
SPECKVignette |
Package source: | SPECK_1.0.0.tar.gz |
Windows binaries: | r-devel: SPECK_1.0.0.zip, r-release: SPECK_1.0.0.zip, r-oldrel: SPECK_1.0.0.zip |
macOS binaries: | r-release (arm64): SPECK_1.0.0.tgz, r-oldrel (arm64): SPECK_1.0.0.tgz, r-release (x86_64): SPECK_1.0.0.tgz, r-oldrel (x86_64): SPECK_1.0.0.tgz |
Old sources: | SPECK archive |
Reverse imports: | STREAK |
Please use the canonical form https://CRAN.R-project.org/package=SPECK to link to this page.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.