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Bioconductor - LACE

LACE

This is the released version of LACE; for the devel version, see LACE.

Longitudinal Analysis of Cancer Evolution (LACE)

Bioconductor version: Release (3.21)

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] ORCID: 0000-0002-6087-2666 , Fabrizio Angaroni [aut], Davide Maspero [cre, aut], Alex Graudenzi [aut], Luca De Sano [aut] ORCID: 0000-0002-9618-3774 , 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 "4.5") 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")
Details biocViews BiomedicalInformatics, SingleCell, Software, SomaticMutation Version 2.12.0 In Bioconductor since BioC 3.11 (R-4.0) (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 System Requirements URL https://github.com/BIMIB-DISCo/LACE Bug Reports https://github.com/BIMIB-DISCo/LACE See More Package Archives

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

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