LACE

Longitudinal Analysis of Cancer Evolution (LACE)

Bioconductor version: 3.23 · Package version: 2.16.0

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.

Installation

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

BiocManager::install("LACE")

Details

Maintainer	Davide Maspero <d.maspero@campus.unimib.it>
Author	Daniele Ramazzotti [aut] (ORCID: <https://orcid.org/0000-0002-6087-2666>), Fabrizio Angaroni [aut], Davide Maspero [cre, aut], Alex Graudenzi [aut], Luca De Sano [aut] (ORCID: <https://orcid.org/0000-0002-9618-3774>), Gianluca Ascolani [aut]
License	file LICENSE
URL	https://github.com/BIMIB-DISCo/LACE
Bug Reports	https://github.com/BIMIB-DISCo/LACE
Downloads rank	342
Source branch	RELEASE_3_23
biocViews	BiomedicalInformatics, SingleCell, Software, SomaticMutation

Documentation

Download

Source package

Dependencies

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

Suggests: BiocGenerics, BiocStyle, testthat, knitr, rmarkdown