dicepro

1.0.2

Semi-Supervised Deconvolution of Bulk RNA-Seq Data with Hyperparameter Optimization

0packages depend

203downloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Kalidou BAFirst published 2026-06-301 releasesCRAN page ↗GitHub ↗

Performs semi-supervised deconvolution of bulk RNA sequencing (RNA-seq) data. Known cell-type proportions are estimated using supervised methods -- 'CIBERSORTx' (CSx), 'CIBERSORT' (CS), 'FARDEEP' (Fast And Robust DEconvolution of Expression Profiles), and 'DCQ' (Digital Cell Quantifier) -- while unknown components are inferred using non-negative matrix factorization ('NMF') with limited-memory Broyden-Fletcher-Goldfarb-Shanno with bounds ('L-BFGS-B') optimization. Hyperparameters are selected automatically using a Pareto-frontier-based approach with knee-point detection, allowing application when the reference signature matrix is incomplete. More details about 'DICEpro' can be found in Ba et al. (2026) doi:10.64898/2026.06.17.732876.

Install

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

install.packages("dicepro", 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("kalidouBA/dicepro")

Development version from kalidouBA/dicepro. 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-dicepro

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: 4.6 min · r-devel-linux-x86_64-fedora-gcc

Code health

Yes

Tests · ratio 0.02

not tracked

Coverage

100%

Documentation · exports

Yes

Vignettes

Yes

README

Dependencies · direct

Check history

OK2026-07-01
7 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Downloads

203

CRAN downloads in the past year

Rank #24,216 · ~1/day · ~17/mo

Releases R versions

Daily download trend is not available in this view yet.

20330 days

20390 days

2031 year

Compare downloads with other packages →

Also on3 r2u

Repository

GitHub ↗ kalidouba/dicepro

5Stars

0Forks

1Open issues

1Open PRs

0Releases

285Commits

abundance-estimationcibersortxdcqdeconvolutioniterative-methodsnmf-matrix-factorizationrrna-seq-analysis

285 commits · 0% stars, 30d

Stars over time

2025-06-20 · 32026-07-07 · 5

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (11)

Rcpp lbfgsb3c KraljicMatrix ggplot2 patchwork FARDEEP ComICS lme4 e1071 preprocessCoreparallel

LinkingTo (2)

Rcpp RcppEigen

Suggests (3)

knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

R 5,072 (64%)Rd 1,747 (22%)Vignettes 919 (12%)C++ 161 (2%)

Code characteristics

Object systems

S32

Cyclomatic complexity: 3.0 median / 18 max
Test cases: 1 / 0.02 per code line
Documented parameters: 94%

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

66 23 exported

Complexity

4.6 avg / 18 max

Call network

66 nodes / 56 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)

Kalidou BA

Author, Maintainer

Authors (2)

Kalidou BA

Author, Maintainer

Boris P. Hejblum

Author

Release timeline

1 release. R releases are shown for context.

1.0.2Latest
2026-06-30 · current release
R
R 4.6.0 released · 2026-04-24

Package metadata

First published: 2026-06-30
Total releases: 1 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1.0
Bundled data: 1.7 MB / 2 files
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet