Package: LACE 2.9.0
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:
LACE_2.9.0.tar.gz
LACE_2.9.0.zip(r-4.5)LACE_2.9.0.zip(r-4.4)LACE_2.9.0.zip(r-4.3)
LACE_2.9.0.tgz(r-4.4-any)LACE_2.9.0.tgz(r-4.3-any)
LACE_2.9.0.tar.gz(r-4.5-noble)LACE_2.9.0.tar.gz(r-4.4-noble)
LACE_2.9.0.tgz(r-4.4-emscripten)LACE_2.9.0.tgz(r-4.3-emscripten)
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')) |
Bug tracker:https://github.com/bimib-disco/lace/issues
- 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-2.9.0(bioc 3.20)LACE-2.8.0(bioc 3.19)
Last updated 2 months agofrom:da83021ac1
Exports:compute.mutation.distancecompute.variants.error.ratesLACElacedataLACEviewlongitudinal.tree.plot
Dependencies:abindAnnotationDbiaskpassassertthatbackportsbase64encBiobaseBiocFileCacheBiocGenericsbiomaRtBiostringsbitbit64blobbslibbspluscachemcallrcheckmateclicliprcodetoolscolorspacecommoncommonmarkconfigrcpp11crayoncrosstalkcurldata.tabledata.treeDBIdbplyrDelayedArraydigestdoParalleldplyrDTellipsisevaluatefansifarverfastmapfilelockfontawesomeforcatsforeachfsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2igraphiniIRangesisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglaterlatticelazyevallearnrlifecyclelogrlubridatemagrittrmarkdownMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrpngprettyunitsprocessxprogresspromisespspurrrR6rappdirsRColorBrewerRcppRcppArmadilloRcppGSLRcppParallelRcppTOMLRcppZigguratreadrrenvRfastrlangrmarkdownrprojrootRSQLiteS4ArraysS4VectorssassscalesshinyshinyBSshinydashboardshinyFilesshinyjsshinythemesshinyvalidatesortablesourcetoolsSparseArraystringistringrSummarizedExperimentsvglitesyssystemfontstibbletidyrtidyselecttimechangetinytextzdbUCSC.utilsutf8vctrsviridisLitevroomwithrxfunxml2xtableXVectoryamlzlibbioc
Introduction
Rendered fromv1_introduction.Rmdusingknitr::rmarkdownon Jun 30 2024.Last update: 2023-04-16
Started: 2023-04-16
LACE-interface
Rendered fromv3_LACE_interface.Rmdusingknitr::rmarkdownon Jun 30 2024.Last update: 2023-04-16
Started: 2023-04-16
Running LACE
Rendered fromv2_running_LACE.Rmdusingknitr::rmarkdownon Jun 30 2024.Last update: 2023-04-16
Started: 2023-04-16
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| compute.mutation.distance | compute.mutation.distance |
| compute.variants.error.rates | compute.variants.error.rates |
| 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. | inference |
| LACE | LACE |
| LACE Interface | lace_interface |
| lacedata | lacedata |
| LACE Processing and Analysis Interface | LACEview |
| Mutation data from Rambow, Florian, et al. "Toward minimal residual disease-directed therapy in melanoma." Cell 174.4 (2018): 843-855. | longitudinal_sc_variants |
| longitudinal.tree.plot | longitudinal.tree.plot |
