Package: SPECK
Type: Package
Title: Receptor Abundance Estimation using Reduced Rank Reconstruction
        and Clustered Thresholding
Version: 1.0.1
Authors@R: c(
    person("H. Robert", "Frost", email = "hildreth.r.frost@dartmouth.edu", role = c("aut")),
    person("Azka", "Javaid", email = "azka.javaid.gr@dartmouth.edu", role = c("aut", "cre")))
Maintainer: Azka Javaid <azka.javaid.gr@dartmouth.edu>
Description: 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>.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.3.2
Suggests: ggplot2, gridExtra, knitr, rmarkdown, SeuratObject, usethis
VignetteBuilder: knitr
Depends: R (>= 3.5)
Imports: Ckmeans.1d.dp, magrittr, Matrix (>= 1.6.1.1), rsvd, Seurat
NeedsCompilation: no
Packaged: 2025-10-05 15:46:20 UTC; azkajavaid
Author: H. Robert Frost [aut],
  Azka Javaid [aut, cre]
Repository: CRAN
Date/Publication: 2025-10-05 16:30:02 UTC
Built: R 4.4.3; ; 2026-01-12 21:59:09 UTC; windows
