CRAN/E | DWLS

DWLS

Gene Expression Deconvolution Using Dampened Weighted Least Squares

Installation

About

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: for more information about the development of 'DWLS' and the methods behind our functions.

github.com/sistia01/DWLS
Bug report File report

Key Metrics

Version 0.1.0
R ≥ 3.5.0
Published 2022-05-24 675 days ago
Needs compilation? no
License GPL-2
CRAN checks DWLS results
Language en-US

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Maintainer

Maintainer

Adriana Sistig

adriana.sistig@icahn.mssm.edu

Authors

Daphne Tsoucas

aut

Adriana Sistig

aut / cre

Material

README
NEWS
Reference manual
Package source

macOS

r-release

arm64

r-oldrel

arm64

r-release

x86_64

r-oldrel

x86_64

Windows

r-devel

x86_64

r-release

x86_64

r-oldrel

x86_64

Depends

R ≥ 3.5.0

Imports

quadprog
reshape
Seurat
ROCR
varhandle
dplyr
stats
utils
e1071
MAST
SummarizedExperiment

Suggests

testthat ≥ 3.0.0
Matrix ≥ 1.3.3