LACE

Bioc current

Longitudinal Analysis of Cancer Evolution (LACE)

v2.16.0 · software · file LICENSE

View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.11 · Apr 28, 2020

Current · Requires R 4.6

1.0 In 13 of 49 releases 3.23

Description

LACE is an algorithmic framework that processes single-cell somatic mutation profiles from cancer samples collected at different time points and in distinct experimental settings, to produce longitudinal models of cancer evolution. The approach solves a Boolean Matrix Factorization problem with phylogenetic constraints, by maximizing a weighed likelihood function computed on multiple time points.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

41 6 exported

Complexity

9.4 avg / 93 max

Call network

41 nodes / 32 edges

Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.

Call graph

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Lowest coverage

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

Code

Structure

Lines of code

4,744

Files

Compiled share

Has compiled src

Language breakdown

R 3,793 (80%)Tests 14 (0.3%)Docs 469 (9.9%)Vignettes 468 (9.9%)

API

Exported functions

Internal functions

Testing & CI

Has tests

Yes

Test-to-code ratio

0.00

testthat edition

–

CI present

Yes

CI type

["github-actions"]

PR gated

Yes

Docs

Roxygen coverage

100%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

100%

Unsafe pattern score

Dep constraint coverage

Secret pattern count

Bundled 3rd-party code

2 items

Portability & License

Min R version

4.2.0

System requirements

–

C++ standard

–

License

file LICENSE

License flags

SPDX valid, not OSI

History

Versions

First release

2020-04-27

Latest release

2026-04-28

Avg cadence

182 days

Cold removal rate

100%

Dep drift

LOC over versions

Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.

Documentation

READMEYes · 517 wordsVignettesYes · dynamicpkgdown siteYesNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Topics

Software › ResearchField › BiomedicalInformatics

Software › Technology › SingleCell

Software › BiologicalQuestion › SomaticMutation

People

Davide Maspero maintainer author
Fabrizio Angaroni author
Gianluca Ascolani author
Luca De Sano author
Alex Graudenzi author
Daniele Ramazzotti author

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