LACE

DOI: 10.18129/B9.bioc.LACE    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see LACE.

Longitudinal Analysis of Cancer Evolution (LACE)

Bioconductor version: 3.13

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.

Author: Daniele Ramazzotti [aut] , Fabrizio Angaroni [aut], Davide Maspero [cre, aut], Alex Graudenzi [aut], Luca De Sano [ctb]

Maintainer: Davide Maspero <d.maspero at campus.unimib.it>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("LACE")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("LACE")

 

PDF	R Script	LACE
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	BiomedicalInformatics, SingleCell, Software, SomaticMutation
Version	1.4.0
In Bioconductor since	BioC 3.11 (R-4.0) (1.5 years)
License	file LICENSE
Depends	R (>= 4.0.0)
Imports	data.tree, graphics, grDevices, igraph, parallel, RColorBrewer, Rfast, stats, SummarizedExperiment, utils
LinkingTo
Suggests	BiocGenerics, BiocStyle, testthat, knitr
SystemRequirements
Enhances
URL	https://github.com/BIMIB-DISCo/LACE
BugReports	https://github.com/BIMIB-DISCo/LACE
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	LACE_1.4.0.tar.gz
Windows Binary	LACE_1.4.0.zip
macOS 10.13 (High Sierra)	LACE_1.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/LACE
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/LACE
Package Short Url	https://bioconductor.org/packages/LACE/
Package Downloads Report	Download Stats