Package: DWLS
Type: Package
Title: Gene Expression Deconvolution Using Dampened Weighted Least
        Squares
Version: 0.1.0
Authors@R: 
    c(person("Daphne", "Tsoucas", email = "dtsoucas@gmail.com", role = "aut"),
    person("Adriana", "Sistig", email = "adriana.sistig@icahn.mssm.edu", 
        role = c("aut","cre")))
Maintainer: Adriana Sistig <adriana.sistig@icahn.mssm.edu>
Description: The rapid development of single-cell transcriptomic
        technologies has helped uncover the cellular heterogeneity
        within cell populations. However, bulk RNA-seq continues to be
        the main workhorse for quantifying gene expression levels due
        to technical simplicity and low cost. To most effectively
        extract information from bulk data given the new knowledge
        gained from single-cell methods, we have developed a novel
        algorithm to estimate the cell-type composition of bulk data
        from a single-cell RNA-seq-derived cell-type signature.
        Comparison with existing methods using various real RNA-seq
        data sets indicates that our new approach is more accurate and
        comprehensive than previous methods, especially for the
        estimation of rare cell types. More importantly,our method can
        detect cell-type composition changes in response to external
        perturbations, thereby providing a valuable, cost-effective
        method for dissecting the cell-type-specific effects of drug
        treatments or condition changes. As such, our method is
        applicable to a wide range of biological and clinical
        investigations. Dampened weighted least squares ('DWLS') is an
        estimation method for gene expression deconvolution, in which
        the cell-type composition of a bulk RNA-seq data set is
        computationally inferred. This method corrects common biases
        towards cell types that are characterized by highly expressed
        genes and/or are highly prevalent, to provide accurate
        detection across diverse cell types. See:
        <https://www.nature.com/articles/s41467-019-10802-z.pdf> for
        more information about the development of 'DWLS' and the
        methods behind our functions.
URL: https://github.com/sistia01/DWLS
BugReports: https://github.com/sistia01/DWLS/issues
Depends: R (>= 3.5.0)
Imports: quadprog, reshape, Seurat, ROCR, varhandle, dplyr, stats,
        utils, e1071, MAST, SummarizedExperiment
License: GPL-2
Encoding: UTF-8
Language: en-US
LazyData: true
LazyDataCompression: xz
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.2
Suggests: testthat (>= 3.0.0), Matrix (>= 1.3.3)
Config/testthat/edition: 3
Config/pak/sysreqs: cmake libglpk-dev make libicu-dev libpng-dev
        libuv1-dev libxml2-dev libssl-dev python3 zlib1g-dev
Repository: https://sistia01.r-universe.dev
Date/Publication: 2022-05-19 13:36:10 UTC
RemoteUrl: https://github.com/sistia01/dwls
RemoteRef: HEAD
RemoteSha: e4c857bac7bc50bdf3373b39e8e281c3d5bc1b6a
NeedsCompilation: no
Packaged: 2026-10-04 08:27:54 UTC; root
Author: Daphne Tsoucas [aut],
  Adriana Sistig [aut, cre]