Package: ELViS 1.4.0

Jin-Young Lee

ELViS: An R Package for Estimating Copy Number Levels of Viral Genome Segments Using Base-Resolution Read Depth Profile

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.

Authors: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]

ELViS_1.4.0.tar.gz
ELViS_1.4.0.zip(r-4.7)ELViS_1.4.0.zip(r-4.6)ELViS_1.4.0.zip(r-4.5)
ELViS_1.4.0.tgz(r-4.6-any)ELViS_1.4.0.tgz(r-4.5-any)
ELViS_1.4.0.tar.gz(r-4.7-any)ELViS_1.4.0.tar.gz(r-4.6-any)
ELViS_1.4.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
ELViS/json (API)
NEWS

# Install 'ELViS' in R:
install.packages('ELViS', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/hyochoi/elvis/issues

Datasets:

On BioConductor:ELViS-1.5.0(bioc 3.24)ELViS-1.4.0(bioc 3.23)

copynumbervariationcoveragegenomicvariationbiomedicalinformaticssequencingnormalizationvisualizationclustering

4.81 score 8 scripts 236 downloads 11 exports 125 dependencies

Last updated from:185e850e5e (on RELEASE_3_23). Checks:1 NOTE, 9 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksNOTE219
linux-devel-x86_64OK521
source / vignettesOK331
linux-release-x86_64OK527
macos-release-arm64OK338
macos-oldrel-arm64OK386
windows-develOK867
windows-releaseOK427
windows-oldrelOK1051
wasm-releaseOK167

Exports:coord_to_grngcoord_to_lstdepth_histfilt_samplesgene_cn_heatmapsget_depth_matrixget_new_baselineintegrative_heatmapnorm_funplot_pileUp_multisamplerun_ELViS

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobcachemcigarillocirclizecliclueclustercodetoolscolorspaceComplexHeatmapcpp11crayoncurldata.tableDBIdbplyrDelayedArraydigestdoParalleldplyrfarverfastmapfilelockforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesGetoptLongggplot2GlobalOptionsgluegtableherehmshttrhttr2igraphIRangesisobanditeratorsjsonliteKEGGRESTlabelinglambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpatchworkpillarpkgconfigplyrpngprettyunitsprogresspurrrR6rappdirsRColorBrewerRcppRcppArmadilloRcppTOMLRCurlreshape2restfulrreticulateRhtslibrjsonrlangrprojrootRsamtoolsRSQLitertracklayerS4ArraysS4VectorsS7scalessegclust2dSeqinfoshapesnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttxdbmakerUCSC.utilsutf8uuidvctrsviridisLitewithrXMLxml2XVectoryamlzoo

ELViS Vignette

Hyo Young Choi, Jin-Young Lee, Jeremiah R. Holt, Katherine A. Hoadley, D. Neil Hayes

Rendered fromELViS_Toy_Example.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2025-09-05
Started: 2025-02-28