Package: ELViS 1.5.0

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_1.5.0.tar.gz
ELViS_1.5.0.zip(r-4.7)ELViS_1.5.0.zip(r-4.6)ELViS_1.5.0.zip(r-4.5)
ELViS_1.5.0.tgz(r-4.6-any)ELViS_1.5.0.tgz(r-4.5-any)
ELViS_1.5.0.tar.gz(r-4.7-any)ELViS_1.5.0.tar.gz(r-4.6-any)
ELViS_1.5.0.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.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 126 dependencies

Last updated from:a918785854. Checks:1 NOTE, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE206
linux-devel-x86_64OK490
source / vignettesOK378
linux-release-x86_64OK528
macos-release-arm64OK273
macos-oldrel-arm64OK304
windows-develOK747
windows-releaseOK424
windows-oldrelOK713
wasm-releaseOK183

Exports:coord_to_grngcoord_to_lstdepth_histfilt_samplesgene_cn_heatmapsget_depth_matrixget_new_baselineintegrative_heatmapnorm_funplot_pileUp_multisamplerun_ELViS

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobcachemcigarillocirclizecliclueclustercodetoolscolorspaceComplexHeatmapcpp11crayoncurldata.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 30 2026.

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