Package: Virusparies 1.1.0

Virusparies: Visualize and Process Output from 'VirusHunterGatherer'

A collection of tools for downstream analysis of 'VirusHunterGatherer' output. Processing of hittables and plotting of results, enabling better interpretation, is made easier with the provided functions.

Authors:Ruff Sergej [aut, cre], Lauber Chris [ctb], Chong Li Chuin [ctb]

Virusparies_1.1.0.tar.gz
Virusparies_1.1.0.zip(r-4.5)Virusparies_1.1.0.zip(r-4.4)Virusparies_1.1.0.zip(r-4.3)
Virusparies_1.1.0.tgz(r-4.4-any)Virusparies_1.1.0.tgz(r-4.3-any)
Virusparies_1.1.0.tar.gz(r-4.5-noble)Virusparies_1.1.0.tar.gz(r-4.4-noble)
Virusparies_1.1.0.tgz(r-4.4-emscripten)Virusparies_1.1.0.tgz(r-4.3-emscripten)
|Virusparies.html✨
Virusparies/json (API)

# Install 'Virusparies' in R:

install.packages('Virusparies', repos = c('https://sergejruff.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/sergejruff/virusparies/issues

On CRAN:

bioinformatics data-driven discover discovery ggplot2 graphical-table hidden-markov-model hmmlearn plot r-programming summary-statistics virus virus-discovery virus-scanning virusgatherer virushunter virushuntergatherer visualization

4.47 score 1 stars 28 scripts 49 downloads 20 exports 88 dependencies

Last updated 1 days agofrom:47fbce70d1. Checks:ERROR: 1 OK: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	FAIL	Nov 17 2024
R-4.5-win	OK	Nov 17 2024
R-4.5-linux	OK	Nov 17 2024
R-4.4-win	OK	Nov 17 2024
R-4.4-mac	OK	Nov 17 2024
R-4.3-win	OK	Nov 17 2024
R-4.3-mac	OK	Nov 17 2024

Exports:CombineHittables Current_ICTV ExportVirusDataFrame ExportVirusGt ExportVirusPlot ImportVirusTable New_ICTV SummarizeViralStats VgConLenViolin VhgAddPhylum VhgBoxplot VhgGetSubject VhgIdenFacetedScatterPlot VhgIdentityScatterPlot VhgPreprocessTaxa VhgRunsBarplot VhgRunsTable VhgSubsetHittable VhgSumHitsBarplot VhgTabularRasa

Dependencies:AsioHeaders base64enc bigD bit bit64 bitops bslib cachem chromote cli clipr colorspace commonmark cowplot cpp11 crayon curl digest dplyr evaluate fansi farver fastmap fontawesome fs generics ggplot2 glue gt gtable highr hms htmltools htmlwidgets isoband jquerylib jsonlite juicyjuice knitr labeling later lattice lifecycle magrittr markdown MASS Matrix memoise mgcv mime munsell nlme pillar pkgconfig prettyunits processx progress promises ps purrr R6 rappdirs RColorBrewer Rcpp reactable reactR readr rlang rmarkdown sass scales stringi stringr tibble tidyr tidyselect tinytex tzdb utf8 V8 vctrs viridisLite vroom websocket withr xfun xml2 yaml

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
CombineHittables: Combine hittables.	CombineHittables
Current_ICTV: Verify the version of ICTV data currently in use.	Current_ICTV
ExportVirusDataFrame: Export processed hittables and summary stats data frames	ExportVirusDataFrame
ExportVirusGt: (Experimental) Export Graphical Tables	ExportVirusGt
Export Virusparies Plots	ExportVirusPlot
Internal function to set default title and cutoff in boxplot function	get_plot_parameters
ImportVirusTable: Import VirusHunterGatherer hittables into R	ImportVirusTable
New_ICTV: Assign Custom ICTV Data for Use in Virusparies	New_ICTV
SummarizeViralStats: Generate summary stats outside of plot functions	SummarizeViralStats
VgConLenViolin: Generate a Violinplot of contig length for each group (Gatherer only)	VgConLenViolin
VhgAddPhylum: extract Phylum information	VhgAddPhylum
VhgBoxplot: Generate box plots comparing E-values,identity or contig length (Gatherer only) for each virus group	VhgBoxplot
VhgGetSubject: Process and Count Viral Subjects within Groups	VhgGetSubject
VhgIdenFacetedScatterPlot: Create a scatter plot of Viral refseq identity vs. -log10 of viral refseq E-value.	VhgIdenFacetedScatterPlot
VhgIdentityScatterPlot: Scatter plot for refseq identity vs -log10 of refseq E-value	VhgIdentityScatterPlot
VhgPreprocessTaxa: preprocess ViralRefSeq_taxonomy elements	VhgPreprocessTaxa
VhgRunsBarplot: Generate a bar plot showing the number of data sets with unique runs found for each Virus group.	VhgRunsBarplot
VhgRunsTable: Generate a gt summary table of unique runs for each virus group	VhgRunsTable
VhgSubsetHittable: Filter VirusHunter and VirusGatherer hittables	VhgSubsetHittable
VhgSumHitsBarplot: Generate a bar plot showing the sum of reads/contigs for each virus family	VhgSumHitsBarplot
VhgTabularRasa: Generate Custom Formatted Graphical Tables	VhgTabularRasa
Virusparies Package	Virusparies-package Virusparies