Package: LACE 2.11.0

Davide Maspero

LACE: Longitudinal Analysis of Cancer Evolution (LACE)

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.

Authors:Daniele Ramazzotti [aut], Fabrizio Angaroni [aut], Davide Maspero [cre, aut], Alex Graudenzi [aut], Luca De Sano [aut], Gianluca Ascolani [aut]

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LACE.pdf |LACE.html✨
LACE/json (API)
NEWS

# Install 'LACE' in R:
install.packages('LACE', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/bimib-disco/lace/issues

Datasets:
  • inference - Results obtained with the function LACE on the provided input data from Rambow, Florian, et al. "Toward minimal residual disease-directed therapy in melanoma." Cell 174.4 (2018): 843-855.
  • longitudinal_sc_variants - Mutation data from Rambow, Florian, et al. "Toward minimal residual disease-directed therapy in melanoma." Cell 174.4 (2018): 843-855.

On BioConductor:LACE-2.9.1(bioc 3.20)LACE-2.8.0(bioc 3.19)

biomedicalinformaticssinglecellsomaticmutation

7.83 score 15 stars 3 scripts 376 downloads 29 mentions 6 exports 156 dependencies

Last updated 25 days agofrom:c6d296d70f. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winOKOct 31 2024
R-4.5-linuxOKOct 30 2024
R-4.4-winOKOct 31 2024
R-4.4-macOKOct 31 2024
R-4.3-winOKOct 30 2024
R-4.3-macOKOct 31 2024

Exports:compute.mutation.distancecompute.variants.error.ratesLACElacedataLACEviewlongitudinal.tree.plot

Dependencies:abindAnnotationDbiaskpassassertthatbackportsbase64encBiobaseBiocFileCacheBiocGenericsbiomaRtBiostringsbitbit64blobbslibbspluscachemcallrcheckmateclicliprcodetoolscolorspacecommoncommonmarkconfigrcpp11crayoncrosstalkcurldata.tabledata.treeDBIdbplyrDelayedArraydigestdoParalleldplyrDTellipsisevaluatefansifarverfastmapfilelockfontawesomeforcatsforeachfsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2igraphiniIRangesisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglaterlatticelazyevallearnrlifecyclelogrlubridatemagrittrmarkdownMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrpngprettyunitsprocessxprogresspromisespspurrrR6rappdirsRColorBrewerRcppRcppArmadilloRcppGSLRcppParallelRcppTOMLRcppZigguratreadrrenvRfastrlangrmarkdownrprojrootRSQLiteS4ArraysS4VectorssassscalesshinyshinyBSshinydashboardshinyFilesshinyjsshinythemesshinyvalidatesortablesourcetoolsSparseArraystringistringrSummarizedExperimentsvglitesyssystemfontstibbletidyrtidyselecttimechangetinytextzdbUCSC.utilsutf8vctrsviridisLitevroomwithrxfunxml2xtableXVectoryamlzlibbioc

Introduction

Daniele Ramazzotti, Fabrizio Angaroni, Davide Maspero, Alex Graudenxi, Luca De Sano, Gianluca Ascolani

Rendered fromv1_introduction.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2023-04-16
Started: 2023-04-16

LACE-interface

Daniele Ramazzotti, Fabrizio Angaroni, Davide Maspero, Alex Graudenxi, Luca De Sano, Gianluca Ascolani

Rendered fromv3_LACE_interface.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2023-04-16
Started: 2023-04-16

Running LACE

Daniele Ramazzotti, Fabrizio Angaroni, Davide Maspero, Alex Graudenxi, Luca De Sano, Gianluca Ascolani

Rendered fromv2_running_LACE.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2023-04-16
Started: 2023-04-16