LACE
This is the development version of LACE; for the stable release version, see LACE.
Longitudinal Analysis of Cancer Evolution (LACE)
Bioconductor version: Development (3.20)
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")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 | 2.9.1 |
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_2.9.1.tar.gz |
Windows Binary | LACE_2.9.1.zip |
macOS Binary (x86_64) | LACE_2.9.1.tgz |
macOS Binary (arm64) | LACE_2.9.1.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 |