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LACE

This is the development version of LACE; for the stable release version, see LACE.

Longitudinal Analysis of Cancer Evolution (LACE)


Bioconductor version: Development (3.19)

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>

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

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
Introduction HTML R Script
LACE-interface HTML R Script
Running LACE HTML R Script
Reference Manual PDF

Details

biocViews BiomedicalInformatics, SingleCell, Software, SomaticMutation
Version 2.7.3
In Bioconductor since BioC 3.11 (R-4.0) (4 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
System Requirements
URL https://github.com/BIMIB-DISCo/LACE
Bug Reports https://github.com/BIMIB-DISCo/LACE
See More
Suggests BiocGenerics, BiocStyle, testthat, knitr, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package LACE_2.7.3.tar.gz
Windows Binary LACE_2.7.3.zip (64-bit only)
macOS Binary (x86_64) LACE_2.7.3.tgz
macOS Binary (arm64)
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