ELViS
This is the development version of ELViS; for the stable release version, see ELViS.
All Bioconductor versions of ELViS
3.24 (devel), 3.23 (release), 3.22, 3.21
An R Package for Estimating Copy Number Levels of Viral Genome Segments Using Base-Resolution Read Depth Profile
Bioconductor version: 3.24 · Package version: 1.5.0
Base-resolution copy number analysis of viral genome. Utilizes base-resolution read depth data over viral genome to find copy number segments with two-dimensional segmentation approach. Provides publish-ready figures, including histograms of read depths, coverage line plots over viral genome annotated with copy number change events and viral genes, and heatmaps showing multiple types of data with integrative clustering of samples.
Author: Hyo Young Choi [aut, cph] 
, Jin-Young Lee [aut, cre, cph] , Xiaobei Zhao [ctb] , Jeremiah R. Holt [ctb] , Katherine A. Hoadley [aut] , D. Neil Hayes [aut, fnd, cph]
Maintainer: Jin-Young Lee <jlee307 at uthsc.edu>
Citation
From within R, enter citation("ELViS"):
Hyo Young Choi, Jin-Young Lee, Katherine A. Hoadley, D. Neil Hayes. ELViS: An R Package for Estimating Copy Number Levels of Viral Genome Segments Using Base-Resolution Read Depth Profile. doi:10.18129/B9.bioc.ELViS, R package version 1.5.0, https://bioconductor.org/packages/ELViS.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("ELViS")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.5.0 |
| License | MIT + file LICENSE |
| URL | https://github.com/hyochoi/ELViS |
| Bug Reports | https://github.com/hyochoi/ELViS/issues |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.21 (R-4.5) (1 year) |
| Downloads rank | 1991 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | BiomedicalInformatics, Clustering, CopyNumberVariation, Coverage, GenomicVariation, Normalization, Sequencing, Software, Visualization |
| Package Short Url | https://bioconductor.org/packages/ELViS/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("ELViS")| ELViS Vignette | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | ELViS_1.5.0.tar.gz |
| Windows binary (x86_64) | ELViS_1.5.0.zip |
| macOS binary (arm64) | ELViS_1.5.0.tgz |
| macOS binary (x86_64) | ELViS_1.5.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ELViS |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ELViS |
| Package Downloads Report | Download Stats |
Dependencies
Depends: R (>= 4.5.0)
Imports: reticulate, BiocGenerics, circlize, ComplexHeatmap, data.table, dplyr, GenomicFeatures, GenomicRanges, ggplot2, glue, graphics, grDevices, igraph, IRanges, magrittr, memoise, methods, parallel, patchwork, scales, segclust2d, stats, stringr, txdbmaker, utils, uuid, zoo
Suggests: Rsamtools, BiocManager, knitr, testthat (>= 3.0.0)