LACE

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see LACE.

Longitudinal Analysis of Cancer Evolution (LACE)


Bioconductor version: 3.16

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

Details

biocViews BiomedicalInformatics, SingleCell, Software, SomaticMutation
Version 2.2.0
In Bioconductor since BioC 3.11 (R-4.0) (4 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, shinyvalidate, shiny, shinythemes, shinyFiles, shinyjs, shinyBS, shinydashboard, biomaRt, callr, logr
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_2.2.0.tar.gz
Windows Binary LACE_2.2.0.zip
macOS Binary (x86_64) LACE_2.2.0.tgz
macOS Binary (arm64) LACE_2.2.0.tgz
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
Old Source Packages for BioC 3.16 Source Archive