ELViS
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
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ELViS")Details
| Maintainer | Jin-Young Lee <jlee307@uthsc.edu> |
| Author | Hyo Young Choi [aut, cph] (ORCID: <https://orcid.org/0000-0002-7627-8493>), Jin-Young Lee [aut, cre, cph] (ORCID: <https://orcid.org/0000-0002-5366-7488>), Xiaobei Zhao [ctb] (ORCID: <https://orcid.org/0000-0002-5277-0846>), Jeremiah R. Holt [ctb] (ORCID: <https://orcid.org/0000-0002-5201-5015>), Katherine A. Hoadley [aut] (ORCID: <https://orcid.org/0000-0002-1216-477X>), D. Neil Hayes [aut, fnd, cph] (ORCID: <https://orcid.org/0000-0001-6203-7771>) |
| License | MIT + file LICENSE |
| URL | https://github.com/hyochoi/ELViS |
| Bug Reports | https://github.com/hyochoi/ELViS/issues |
| 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/ |
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.
Documentation
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 |
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)