LACE

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11

Longitudinal Analysis of Cancer Evolution (LACE)

Bioconductor version: Release (3.23)

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")):

Daniele Ramazzotti, Fabrizio Angaroni, Davide Maspero, Alex Graudenzi, Luca De Sano, Gianluca Ascolani. LACE: Longitudinal Analysis of Cancer Evolution (LACE). doi:10.18129/B9.bioc.LACE, R package version 2.16.0, https://bioconductor.org/packages/LACE.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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")

Introduction	HTML	R Script
Running LACE	HTML	R Script
LACE-interface	HTML	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	BiomedicalInformatics, SingleCell, Software, SomaticMutation
Version	2.16.0
In Bioconductor since	BioC 3.11 (R-4.0) (6.5 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

Suggests	BiocGenerics, BiocStyle, testthat, knitr, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	LACE_2.16.0.tar.gz
Windows Binary (x86_64)	LACE_2.16.0.zip
macOS Binary (big-sur-x86_64)	LACE_2.16.0.tgz
macOS Binary (sonoma-arm64)	LACE_2.16.0.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