LACHESIS
Functions used to analyze early tumor evolution from whole genome sequencing data
Bioconductor version: 3.23 · Package version: 1.0.0
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("LACHESIS") Details
| Maintainer | Verena Körber <verena.korber@ndcls.ox.ac.uk> |
| Author | Verena Körber [aut, cre] (ORCID: <https://orcid.org/0009-0005-3888-2648>), Anand Mayakonda [aut], Maximilia Eggle [aut] |
| License | GPL (>= 3) |
| URL | https://github.com/VerenaK90/LACHESIS |
| Bug Reports | https://github.com/VerenaK90/LACHESIS/issues |
| Downloads rank | 85 |
| Source branch | RELEASE_3_23 |
| biocViews | Sequencing, Software, SomaticMutation, StatisticalMethod, Survival, TimeCourse, WholeGenome |
Documentation
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Dependencies
Depends: R (>= 4.3)
Imports: data.table, vcfR, tidyr, stats, utils, graphics, grDevices, ggplot2, gridExtra, survival, survminer, RColorBrewer, Biostrings
Suggests: BSgenome.Hsapiens.UCSC.hg19, BiocStyle, Cairo, rmarkdown, knitr, R.utils, tinytest, GenomeInfoDb, GenomicRanges, IRanges, MutationalPatterns, magick