DWLS

0.1.0

Gene Expression Deconvolution Using Dampened Weighted Least Squares

0packages depend

3.5Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Adriana SistigFirst published 2022-05-241 releasesCRAN page ↗GitHub ↗

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.

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("DWLS", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("sistia01/DWLS")

Development version from sistia01/DWLS. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-dwls

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

Health

CRAN checks

13OK

Slowest check: 12.2 min · r-devel-linux-x86_64-fedora-gcc

Code health

Yes

Tests · ratio 0.01

not tracked

Coverage

100%

Documentation · exports

None

Vignettes

Yes

README

Dependencies · direct

Check history

OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-10
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-05-03
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 2 earlier snapshots

ERROR2026-04-09
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Downloads

3.5K

CRAN downloads in the past year

Rank #10,804 · ~10/day · ~294/mo

Releases R versions

Daily download trend is not available in this view yet.

39030 days

99490 days

3.5K1 year

Compare downloads with other packages →

Also on98 r2u767 bioconda

Repository

GitHub ↗ sistia01/dwls

5Stars

1Forks

3Open issues

0Open PRs

0Releases

Stars over time

2025-05-13 · 32026-07-07 · 5

Dependencies

Declared dependencies

10 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (11)

quadprog reshape Seurat ROCR varhandle dplyrstatsutilse1071 MAST SummarizedExperiment

LinkingTo (0)

none

Suggests (2)

testthatMatrix

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

R 1,424 (57%)Rd 1,091 (43%)

Code characteristics

Cyclomatic complexity: 1.0 median / 10 max
Test cases: 2 / 0.01 per code line
Documented parameters: 100%

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

17 17 exported

Complexity

3 avg / 10 max

Call network

17 nodes / 9 edges

Test coverage has not been measured for this package yet; nodes fall back to a neutral fill.

Call graph

Open call graph →

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Lowest coverage

Per-function coverage is not measured for this package yet.

People & History

People (2)

Maintainer (1)

Adriana Sistig

Author, Maintainer

Authors (2)

Adriana Sistig

Author, Maintainer

Daphne Tsoucas

Author

Release timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.1.0Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2022-05-24
Total releases: 1 / 4 yrs
License: GPL-2 OSI
Minimum R: ≥ 3.5.0
Bundled data: 145 KB / 1 file
Download size: 172 KB
Installed size: not tracked yet
With dependencies: not tracked yet