LACHESIS
This is the development version of LACHESIS; to use it, please install the devel version of Bioconductor.
Functions used to analyze early tumor evolution from whole genome sequencing data
Bioconductor version: Development (3.23)
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.
Author: Verena Körber [aut, cre]
, Anand Mayakonda [aut], Maximilia Eggle [aut]
Maintainer: Verena Körber <verena.korber at ndcls.ox.ac.uk>
citation("LACHESIS")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("LACHESIS")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("LACHESIS")| LACHESIS - Real-time inference of evolutionary dynamics during tumor initiation based on whole genome sequencing data | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Sequencing, Software, SomaticMutation, StatisticalMethod, Survival, TimeCourse, WholeGenome |
| Version | 0.99.4 |
| In Bioconductor since | BioC 3.23 (R-4.6) |
| License | GPL (>= 3) |
| Depends | R (>= 4.5) |
| Imports | data.table, vcfR, tidyr, stats, utils, graphics, grDevices, ggplot2, gridExtra, survival, survminer, RColorBrewer, Biostrings |
| System Requirements | |
| URL | https://github.com/VerenaK90/LACHESIS |
| Bug Reports | https://github.com/VerenaK90/LACHESIS/issues |
See More
| Suggests | BSgenome.Hsapiens.UCSC.hg19, BiocStyle, Cairo, rmarkdown, knitr, R.utils, tinytest, GenomeInfoDb, GenomicRanges, IRanges, MutationalPatterns, magick |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | LACHESIS_0.99.4.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/LACHESIS |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/LACHESIS |
| Bioc Package Browser | https://code.bioconductor.org/browse/LACHESIS/ |
| Package Short Url | https://bioconductor.org/packages/LACHESIS/ |
| Package Downloads Report | Download Stats |