Package: ELViS 0.99.13

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✨
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-0.99.11(bioc 3.21)

copynumbervariationcoveragegenomicvariationbiomedicalinformaticssequencingnormalizationvisualizationclustering

4.70 score 7 scripts 18 downloads 11 exports 132 dependencies

Last updated 13 days agofrom:ed429d6b20. Checks:7 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 05 2025
R-4.5-winOKMar 05 2025
R-4.5-macOKMar 05 2025
R-4.5-linuxOKMar 05 2025
R-4.4-winOKMar 05 2025
R-4.4-macOKMar 05 2025
R-4.4-linuxOKMar 05 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 fromELViS_Toy_Example.Rmdusingknitr::rmarkdownon Mar 05 2025.

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