LACE

DOI: 10.18129/B9.bioc.LACE    

Longitudinal Analysis of Cancer Evolution (LACE)

Bioconductor version: Release (3.15)

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 "4.2") 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")

 

PDF R Script LACE
PDF R Script LACE 2.0
PDF   Reference Manual
Text   NEWS
Text   LICENSE

Details

biocViews BiomedicalInformatics, SingleCell, Software, SomaticMutation
Version 2.0.0
In Bioconductor since BioC 3.11 (R-4.0) (2.5 years)
License file LICENSE
Depends R (>= 4.1.0)
Imports curl, igraph, foreach, doParallel, sortable, dplyr, 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, shiny, shinythemes, shinyFiles, shinyjs, shinyBS, shinydashboard, biomaRt, callr
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_2.0.0.tar.gz
Windows Binary LACE_2.0.0.zip
macOS 10.13 (High Sierra) LACE_2.0.0.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

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