ELViS
This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see ELViS.
An R Package for Estimating Copy Number Levels of Viral Genome Segments Using Base-Resolution Read Depth Profile
Bioconductor version: 3.21
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 iD ORCID: 0000-0002-7627-8493 , Jin-Young Lee [aut, cre, cph] ORCID iD ORCID: 0000-0002-5366-7488 , Xiaobei Zhao [ctb] ORCID iD ORCID: 0000-0002-5277-0846 , Jeremiah R. Holt [ctb] ORCID iD ORCID: 0000-0002-5201-5015 , Katherine A. Hoadley [aut] ORCID iD ORCID: 0000-0002-1216-477X , D. Neil Hayes [aut, fnd, cph] ORCID iD ORCID: 0000-0001-6203-7771
Maintainer: Jin-Young Lee <jlee307 at uthsc.edu>
citation("ELViS")):
Installation
To install this package, start R (version "4.5") 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")
Details
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Follow Installation instructions to use this package in your R session.