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: 2026-07-02 07:58:56 UTC; root
Author: H. Robert Frost [aut], Azka Javaid [aut, cre]
Repository: https://cran.r-universe.dev
Date/Publication: 2025-10-05 16:30:02 UTC
RemoteUrl: https://github.com/cran/SPECK
RemoteRef: HEAD
RemoteSha: 29b9e202d03fbeb86f185d7a8b183f375e6e1fe4