DCLEAR

1.0.13

Distance Based Cell Lineage Reconstruction

0packages depend

3.1Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Il-Youp KwakFirst published 2021-07-155 releasesCRAN page ↗GitHub ↗

R codes for distance based cell lineage reconstruction. Our methods won both sub-challenges 2 and 3 of the Allen Institute Cell Lineage Reconstruction DREAM Challenge in 2020. References: Gong et al. (2021) doi:10.1016/j.cels.2021.05.008, Gong et al. (2022) doi:10.1186/s12859-022-04633-x.

Install

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

install.packages("DCLEAR", 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("ikwak2/DCLEAR")

Development version from ikwak2/DCLEAR. 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-dclear

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

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Yes

Vignettes

Yes

README

Dependencies · direct

Check history

OK2026-04-22
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Downloads

3.1K

CRAN downloads in the past year

Rank #12,276 · ~8/day · ~256/mo

Releases R versions

Daily download trend is not available in this view yet.

37430 days

86890 days

3.1K1 year

Compare downloads with other packages →

Also on396 r2u

Repository

GitHub ↗ ikwak2/dclear

6Stars

2Forks

1Open issues

0Open PRs

0Releases

258Commits

258 commits · 0% stars, 30d

Stars over time

2023-04-26 · 62026-07-07 · 6

Dependencies

Declared dependencies

19 external dependencies (excludes base and recommended)

Depends (2)

R >= 4.1.0tensorflow

Imports (15)

BiocParallel dplyrMatrixmatrixStats ape phangorn Rcpp igraphmethodspurrr stringr tidyr rBayesianOptimization rlang BiocGenerics

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (3)

knitr rmarkdown markdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

R 1,973 (53%)Rd 1,331 (35%)Vignettes 313 (8%)C++ 136 (4%)

Code characteristics

Object systems

S4 class4S4 generic14S4 method21

Cyclomatic complexity: 1.0 median / 13 max
Documented parameters: 100%

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

27 8 exported

Complexity

2.5 avg / 13 max

Call network

27 nodes / 16 edges

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

Call graph

Open call graph →

Loading call graph…

Lowest coverage

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

People & History

People (2)

Maintainer (1)

Il-Youp Kwak

Author, Maintainer

Authors (2)

Il-Youp Kwak

Author, Maintainer

Wuming Gong

Author

Release timeline

5 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.0.13Latest
2023-09-14 · current release · diff ↗
R
R 4.3.0 released · 2023-04-21
1.0.12
2023-02-16 · diff ↗
1.0.11
2022-11-30 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.0.8
2021-09-03 · diff ↗
1.0.0
2021-07-15
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-07-15
Total releases: 5 / 5 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.1.0
Bundled data: 636 KB / 1 file
Download size: 678 KB
Installed size: not tracked yet
With dependencies: not tracked yet