R Observatory: Metrics for dicepro version 1.0.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

dicepro

1.0.2Package record

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

0packages depend

996downloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Kalidou BACRAN page ↗GitHub ↗Issues ↗

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. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 4.1 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK7 OK2026-07-01

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.2

READMEYes · 540 wordsVignettesYes · 3 · staticNEWSYes · 67% structured · mentions 1.0.2Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 27includes a package overview page
Examples that run: 82%9 run in a plain check · 2 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 48%
Documented parameters: 94%
Return-value docs: 100%
Help pages citing references: 7%

Vignettes (3)

How these are measured

Downloads

996

CRAN downloads in the past year

Rank #19,418 · ~3/day · ~83/mo

Releases R versions

Daily download trend is not available in this view yet.

20730 days

68690 days

9961 year

Compare downloads with other packages →

Also on57 r2u

How downloads are counted

Repository

kalidouba/dicepro ↗Account: kalidouBA

5Stars

0Forks

1Open issues

1Open PRs

0Releases

285Commits

3Commit identities

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

285 commits · Last activity 2026-06-24 · 0% stars, 30d

Responsiveness

not measured

Stars over time

2025-06-20 · 32026-07-07 · 5

How these are measured

PracticesBeta

5 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/kalidouba/dicepro on 2026-10-25.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Docs source (1)

README.Rmd

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Installing dicepro adds 47 packages (24 with compiled code, 39 MB of source tarballs). Heaviest: ggplot2 6.0 MB, lme4 4.3 MB, patchwork 3.2 MB. 1 more not on CRAN is not measured.

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.

How these are counted

Code & Tests

Datasets

People & History

People (2)

Kalidou BA

Author, Maintainer since 1.0.2 (2026)

Boris P. Hejblum

Author

Releases (1)

1.0.2Latest
record
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: 1.8 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("dicepro")

Format

BA, K., & Hejblum, B. P. (2026). dicepro: Semi-Supervised Deconvolution of Bulk RNA-Seq Data with Hyperparameter Optimization (Version 1.0.2) [Computer software]. https://doi.org/10.32614/CRAN.package.dicepro

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for dicepro version 1.0.2 [Data set]. HJJB, LLC. Data release v2026-10-26. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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