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>

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HTML R Script Introduction
HTML R Script LACE-interface
HTML R Script Running LACE
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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
Suggests BiocGenerics, BiocStyle, testthat, knitr, rmarkdown
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