LACE

DOI: 10.18129/B9.bioc.LACE  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see LACE.

Longitudinal Analysis of Cancer Evolution (LACE)

Bioconductor version: 3.17

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 [aut] , Gianluca Ascolani [aut]

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

Installation

To install this package, start R (version "4.3") and enter:

if (!require("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")

 

HTML	R Script	Introduction
HTML	R Script	LACE-interface
HTML	R Script	Running LACE
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	BiomedicalInformatics, SingleCell, Software, SomaticMutation
Version	2.4.0
In Bioconductor since	BioC 3.11 (R-4.0) (3.5 years)
License	file LICENSE
Depends	R (>= 4.2.0)
Imports	curl, igraph, foreach, doParallel, sortable, dplyr, forcats, data.tree, graphics, grDevices, parallel, RColorBrewer, Rfast, stats, SummarizedExperiment, utils, purrr, stringi, stringr, Matrix, tidyr, jsonlite, readr, configr, DT, tools, fs, data.table, htmltools, htmlwidgets, bsplus, shinyvalidate, shiny, shinythemes, shinyFiles, shinyjs, shinyBS, shinydashboard, biomaRt, callr, logr, ggplot2, svglite
LinkingTo
Suggests	BiocGenerics, BiocStyle, testthat, knitr, rmarkdown
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_2.4.0.tar.gz
Windows Binary	LACE_2.4.0.zip
macOS Binary (x86_64)	LACE_2.4.0.tgz
macOS Binary (arm64)	LACE_2.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/LACE
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/LACE
Bioc Package Browser	https://code.bioconductor.org/browse/LACE/
Package Short Url	https://bioconductor.org/packages/LACE/
Package Downloads Report	Download Stats