Package: ELViS 0.99.11

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]

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ELViS.pdf |ELViS.html✨
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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-0.99.10(bioc 3.21)

copynumbervariationcoveragegenomicvariationbiomedicalinformaticssequencingnormalizationvisualizationclustering

4.60 score 7 scripts 1 downloads 11 exports 132 dependencies

Last updated 2 days agofrom:b7ddb52bdf. Checks:6 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 22 2025
R-4.5-winOKFeb 22 2025
R-4.5-macOKFeb 22 2025
R-4.5-linuxOKFeb 22 2025
R-4.4-winOKFeb 22 2025
R-4.4-macOKFeb 22 2025

Exports:coord_to_grngcoord_to_lstdepth_histfilt_samplesgene_cn_heatmapsget_depth_matrixget_new_baselineintegrative_heatmapnorm_funplot_pileUp_multisamplerun_ELViS

Dependencies:abindAnnotationDbiaskpassbasiliskbasilisk.utilsBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobcachemcirclizecliclueclustercodetoolscolorspaceComplexHeatmapcpp11crayoncurldata.tableDBIdbplyrDelayedArraydigestdir.expirydoParalleldplyrfansifarverfastmapfilelockforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesGetoptLongggplot2GlobalOptionsgluegtableherehmshttrhttr2igraphIRangesisobanditeratorsjsonliteKEGGRESTlabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpatchworkpillarpkgconfigplogrplyrpngprettyunitsprogresspurrrR6rappdirsRColorBrewerRcppRcppArmadilloRcppTOMLRCurlreshape2restfulrreticulateRhtslibrjsonrlangrprojrootRsamtoolsRSQLitertracklayerS4ArraysS4Vectorsscalessegclust2dshapesnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttxdbmakerUCSC.utilsutf8uuidvctrsviridisLitewithrXMLxml2XVectoryamlzoo

ELViS Vignette

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

Rendered fromELViSPrecisely_Toy_Example.Rmdusingknitr::rmarkdownon Feb 22 2025.

Last update: 2025-02-18
Started: 2024-10-21