LACE

DOI: 10.18129/B9.bioc.LACE    

Longitudinal Analysis of Cancer Evolution (LACE)

Bioconductor version: Release (3.12)

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>

Citation (from within R, enter citation("LACE")):

Installation

To install this package, start R (version "4.0") 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 1.2.1
In Bioconductor since BioC 3.11 (R-4.0) (0.5 years)
License file LICENSE
Depends R (>= 4.0.0)
Imports 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_1.2.1.tar.gz
Windows Binary LACE_1.2.1.zip
macOS 10.13 (High Sierra) LACE_1.2.1.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
Old Source Packages for BioC 3.12 Source Archive

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