LACE
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see LACE.
Longitudinal Analysis of Cancer Evolution (LACE)
Bioconductor version: 3.19
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("LACE")):
Installation
To install this package, start R (version "4.4") 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 |
| LACE-interface | HTML | R Script |
| Running LACE | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | BiomedicalInformatics, SingleCell, Software, SomaticMutation |
| Version | 2.8.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (4.5 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
| 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_2.8.0.tar.gz |
| Windows Binary (x86_64) | LACE_2.8.0.zip |
| macOS Binary (x86_64) | LACE_2.8.0.tgz |
| macOS Binary (arm64) | LACE_2.8.0.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 |