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✨
DESCRIPTION |NEWS
card.svg |card.png
ELViS/json (API)

# 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:

ELViS_toy_run_result - ELViS Toy Example - Run Result
mtrx_samtools_reticulate - ELViS Toy Example - Base-Resolution Raw Read Depth
total_aligned_base__host_and_virus - ELViS Toy Example - Total Aligned Base
toy_example - ELViS Toy Example - Metadata

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

copynumbervariation coverage genomicvariation biomedicalinformatics sequencing normalization visualization clustering

4.74 score 8 scripts 11 exports 126 dependencies

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

Target	Result	Time
bioc-checks	NOTE	241
linux-devel-x86_64	OK	496
source / vignettes	OK	299
linux-release-x86_64	OK	517
macos-release-arm64	OK	491
macos-oldrel-arm64	OK	292
windows-devel	OK	435
windows-release	OK	466
windows-oldrel	OK	420
wasm-release	OK	197

Exports:coord_to_grng coord_to_lst depth_hist filt_samples gene_cn_heatmaps get_depth_matrix get_new_baseline integrative_heatmap norm_fun plot_pileUp_multisample run_ELViS

Dependencies:abind AnnotationDbi askpass BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt Biostrings bit bit64 bitops blob cachem cigarillo circlize cli clue cluster codetools colorspace ComplexHeatmap cpp11 crayon curl data.table DBI dbplyr DelayedArray digest doParallel dplyr farver fastmap filelock foreach formatR futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges GetoptLong ggplot2 GlobalOptions glue gtable here hms httr httr2 igraph IRanges isoband iterators jsonlite KEGGREST labeling lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime openssl patchwork pillar pkgconfig plyr png prettyunits progress purrr R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppTOML RCurl reshape2 restfulr reticulate Rhtslib rjson rlang rprojroot Rsamtools RSQLite rtracklayer S4Arrays S4Vectors S7 scales segclust2d Seqinfo shape snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect txdbmaker UCSC.utils utf8 uuid vctrs viridisLite withr XML xml2 XVector yaml zoo

ELViS Vignette

Rendered fromELViS_Toy_Example.Rmdusingknitr::rmarkdown

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

Help page	Topics
Convert coordinate string to grng object	coord_to_grng
Convert coordinate string to list of chr,start and end	coord_to_lst
Sample filtering threshold examination plot.	depth_hist
ELViS : An R Package for Estimating Copy Number Levels of Viral Genome Segments Using Base-Resolution Read Depth Profile.	ELViS-package ELViS
ELViS Toy Example - Run Result	ELViS_toy_run_result
Filtering samples based on summary statistic	filt_samples
Gene Copy Number Heatmap	gene_cn_heatmaps
Generate a read depth matrix of positions x samples from input BAM files list	get_depth_matrix
Get new baselines according to criteria user designates	get_new_baseline
Plot heatmaps based on simple integrative clustering of multiple matrices	integrative_heatmap
ELViS Toy Example - Base-Resolution Raw Read Depth	mtrx_samtools_reticulate
Normalization - scaling by certain quantile	norm_fun
Get a list of pile-up plots over multiple samples	plot_pileUp_multisample
Run ELViS using input raw depth matrix	run_ELViS
ELViS Toy Example - Total Aligned Base	total_aligned_base__host_and_virus
ELViS Toy Example - Metadata	toy_example

Package: ELViS 1.5.0

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

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)