Package: LACE 2.17.0

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]

LACE_2.17.0.tar.gz
LACE_2.17.0.zip(r-4.7-any)LACE_2.17.0.zip(r-4.6-any)LACE_2.17.0.zip(r-4.5-any)
LACE_2.17.0.tgz(r-4.6-any)LACE_2.17.0.tgz(r-4.5-any)
LACE_2.17.0.tar.gz(r-4.7-any)LACE_2.17.0.tar.gz(r-4.6-any)
LACE_2.17.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
LACE/json (API)

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

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-2.17.0(bioc 3.24)LACE-2.16.0(bioc 3.23)

biomedicalinformaticssinglecellsomaticmutation

7.68 score 16 stars 5 scripts 557 downloads 29 mentions 6 exports 149 dependencies

Last updated from:ccf646a995. Checks:1 WARNING, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING356
linux-develOK415
source / vignettesOK420
linux-releaseOK424
macos-releaseOK283
macos-oldrelOK207
windows-develOK255
windows-releaseOK486
windows-oldrelOK254
wasm-releaseOK318

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

Dependencies:abindAnnotationDbiaskpassassertthatbackportsbase64encBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsbiomaRtBiostringsbitbit64blobbslibbspluscachemcallrcheckmateclicliprcodetoolscommoncommonmarkconfigrcpp11crayoncrosstalkcurldata.tabledata.treeDBIdbplyrDelayedArraydigestdoParalleldplyrDTevaluatefarverfastmapfilelockfontawesomeforcatsforeachfsgenericsGenomicRangesggplot2gluegtablehighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2igraphiniIRangesisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglaterlatticelazyevallearnrlifecyclelitedownlogrlubridatemagrittrmarkdownMatrixMatrixGenericsmatrixStatsmemoisemimeopensslotelpillarpkgconfigpngprettyunitsprocessxprogresspromisespspurrrR6rappdirsRColorBrewerRcppRcppArmadilloRcppParallelRcppTOMLreadrrenvRfastrlangrmarkdownrprojrootRSQLiteS4ArraysS4VectorsS7sassscalesSeqinfoshinyshinyBSshinydashboardshinyFilesshinyjsshinythemesshinyvalidatesortablesourcetoolsSparseArraystringistringrSummarizedExperimentsvglitesyssystemfontstextshapingtibbletidyrtidyselecttimechangetinytextzdbutf8vctrsviridisLitevroomwithrxfunxml2xtableXVectoryamlzigg

Introduction
Overview | Installing LACE | Debug
Rendered fromv1_introduction.Rmdusingknitr::rmarkdown

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

LACE-interface
Installation of LACE 2.0 R package | Installation of other required softwares | For Windows users, we suggest the following guidelines: | Running LACE 2.0 | Using LACE 2.0 | Interface | Project creation | Sidebar and Demos | Processing interface | Single Cell Metadata | Annotations | Variant filtering | Single cell sampling depth | Selection of relevant variants | Inference | Parameter ranges | Longitudinal display and outputs interface
Rendered fromv3_LACE_interface.Rmdusingknitr::rmarkdown

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

Running LACE
Setup the environement | Inference | Plot
Rendered fromv2_running_LACE.Rmdusingknitr::rmarkdown

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