ELViS
This is thereleased version of ELViS; for the devel version, seeELViS.
An R Package for Estimating Copy Number Levels of Viral Genome Segments Using Base-Resolution Read Depth Profile
Bioconductor version: Release (3.22)
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("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 appropriateBioconductor 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | BiomedicalInformatics,Clustering,CopyNumberVariation,Coverage,GenomicVariation,Normalization,Sequencing,Software,Visualization |
| Version | 1.2.0 |
| In Bioconductor since | BioC 3.21 (R-4.5) (0.5 years) |
| License | MIT + fileLICENSE |
| 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 |
See More
| 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 |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | ELViS_1.2.0.tar.gz |
| Windows Binary (x86_64) | ELViS_1.2.0.zip |
| macOS Binary (x86_64) | ELViS_1.2.0.tgz |
| macOS Binary (arm64) | ELViS_1.2.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ELViS |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ELViS |
| Bioc Package Browser | https://code.bioconductor.org/browse/ELViS/ |
| Package Short Url | https://bioconductor.org/packages/ELViS/ |
| Package Downloads Report | Download Stats |