LACE
This is the released version of LACE; for the devel version, see LACE.
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]
, 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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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 |
| LACE-interface | HTML | R Script |
| Running LACE | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
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 |
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_2.16.0.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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/LACE/ |
| Package Short Url | https://bioconductor.org/packages/LACE/ |
| Package Downloads Report | Download Stats |