LACE
This is thereleased version of LACE; for the devel version, seeLACE.
Longitudinal Analysis of Cancer Evolution (LACE)
Bioconductor version: Release (3.22)
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("LACE")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("LACE")For older versions of R, please refer to the appropriateBioconductor 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 | 2.14.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (5.5 years) |
| License | fileLICENSE |
| 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
FollowInstallation instructions to use this package in your R session.
| Source Package | LACE_2.14.0.tar.gz |
| Windows Binary (x86_64) | LACE_2.14.0.zip |
| macOS Binary (x86_64) | LACE_2.14.0.tgz |
| macOS Binary (arm64) | LACE_2.14.0.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 |