ELViS

This is the released version of ELViS; for the devel version, see ELViS.

All versions

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: Release (3.23)

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] ORCID: 0000-0002-7627-8493 , Jin-Young Lee [aut, cre, cph] ORCID: 0000-0002-5366-7488 , Xiaobei Zhao [ctb] ORCID: 0000-0002-5277-0846 , Jeremiah R. Holt [ctb] ORCID: 0000-0002-5201-5015 , Katherine A. Hoadley [aut] ORCID: 0000-0002-1216-477X , D. Neil Hayes [aut, fnd, cph] ORCID: 0000-0001-6203-7771

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 1.4.0, 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")

BiocManager::install("ELViS")

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("ELViS")

Authoring R Markdown vignettes	HTML	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	BiomedicalInformatics, Clustering, CopyNumberVariation, Coverage, GenomicVariation, Normalization, Sequencing, Software, Visualization
Version	1.4.0
In Bioconductor since	BioC 3.21 (R-4.5) (1.5 years)
License	MIT + file LICENSE
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
System Requirements
URL	https://github.com/hyochoi/ELViS
Bug Reports	https://github.com/hyochoi/ELViS/issues

Suggests	Rsamtools, BiocManager, knitr, testthat (>= 3.0.0)
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	ELViS_1.4.0.tar.gz
Windows Binary (x86_64)	ELViS_1.4.0.zip
macOS Binary (big-sur-x86_64)	ELViS_1.4.0.tgz
macOS Binary (sonoma-arm64)	ELViS_1.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ELViS
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ELViS
Package Short Url	https://bioconductor.org/packages/ELViS/
Package Downloads Report	Download Stats