Package: LACHESIS 1.0.0

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_1.0.0.tar.gz
LACHESIS_1.0.0.zip(r-4.7)LACHESIS_1.0.0.zip(r-4.6)LACHESIS_1.0.0.zip(r-4.5)
LACHESIS_1.0.0.tgz(r-4.6-any)LACHESIS_1.0.0.tgz(r-4.5-any)
LACHESIS_1.0.0.tar.gz(r-4.7-any)LACHESIS_1.0.0.tar.gz(r-4.6-any)
LACHESIS_1.0.0.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-release.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 143 downloads 17 exports 107 dependencies

Last updated from:51c5333675 (on RELEASE_3_23). Checks:8 NOTE, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksNOTE279
linux-devel-x86_64NOTE645
source / vignettesOK478
linux-release-x86_64NOTE726
macos-release-arm64NOTE350
macos-oldrel-arm64NOTE397
windows-develNOTE609
windows-releaseNOTE589
windows-oldrelNOTE580
wasm-releaseOK262

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 29 2026.

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