Package: LACHESIS 1.1.0

Verena Körber

LACHESIS: Functions used to analyze early tumor evolution from whole genome sequencing data

This package provides modalities to analyze tumor evolution from whole genome sequencing data. In particular, it provides estimates of mutation densities at genomic segments and uses these to time the origin of the tumor.

Authors:Verena Körber [aut, cre], Anand Mayakonda [aut], Maximilia Eggle [aut]

LACHESIS_1.1.0.tar.gz
LACHESIS_1.1.0.zip(r-4.7)LACHESIS_1.1.0.zip(r-4.6)LACHESIS_1.1.0.zip(r-4.5)
LACHESIS_1.1.0.tgz(r-4.6-any)LACHESIS_1.1.0.tgz(r-4.5-any)
LACHESIS_1.1.0.tar.gz(r-4.7-any)LACHESIS_1.1.0.tar.gz(r-4.6-any)
LACHESIS_1.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
LACHESIS/json (API)
NEWS

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

Bug tracker:https://github.com/verenak90/lachesis/issues

On BioConductor:LACHESIS-1.1.0(bioc 3.24)LACHESIS-1.0.0(bioc 3.23)

softwarestatisticalmethodtimecoursesequencingwholegenomesurvivalsomaticmutationtumor-evolutionwhole-genome-sequencing

5.65 score 3 stars 7 scripts 143 downloads 17 exports 107 dependencies

Last updated from:1b25ebaaaa. Checks:8 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE243
linux-devel-x86_64NOTE658
source / vignettesOK426
linux-release-x86_64NOTE636
macos-release-arm64NOTE374
macos-oldrel-arm64NOTE359
windows-develNOTE706
windows-releaseNOTE645
windows-oldrelNOTE635
wasm-releaseOK218

Exports:classifyLACHESISclonalMutationCounterestimateClonalityLACHESISMRCAnbImportnormalizeCountsplotClinicalCorrelationsplotClonalityplotDiseaseTrajectoriesplotLachesisplotMutationDensitiesplotNBplotSurvivalplotVAFdistrreadCNVreadVCF

Dependencies:abindapebackportsBiocGenericsBiostringsbootbroomcarcarDatacliclustercolorspacecommonmarkcorrplotcowplotcpp11crayoncurldata.tableDerivdigestdoBydplyrexactRankTestsfarverforecastFormulafracdiffgenericsggplot2ggpubrggrepelggsciggsignifggtextgluegridExtragridtextgtableIRangesisobandjpeglabelinglatticelifecyclelitedownlme4lmtestmagrittrmarkdownMASSMatrixMatrixModelsmaxstatmemusemgcvmicrobenchmarkminqamodelrmvtnormnlmenloptrnnetnumDerivpbkrtestpermutepillarpinfsc50pkgconfigpngpolynompurrrquantregR6rbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreformulasrlangrstatixS4VectorsS7scalesSeqinfoSparseMstringistringrsurvivalsurvminertibbletidyrtidyselecttimeDateurcautf8vcfRvctrsveganviridisLitewithrxfunxml2XVectorzoo

LACHESIS - Real-time inference of evolutionary dynamics during tumor initiation based on whole genome sequencing data

Rendered fromvignette_LACHESIS.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2026-03-16
Started: 2025-01-22