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
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 |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:

bioinformaticsdata-drivendiscoverdiscoveryggplot2graphical-tablehidden-markov-modelhmmlearnplotr-programmingsummary-statisticsvirusvirus-discoveryvirus-scanningvirusgatherervirushuntervirushuntergatherervisualization

4.49 score 1 stars 28 scripts 173 downloads 20 exports 88 dependencies

Last updated 2 months agofrom:58173453dd. Checks:1 ERROR, 7 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesFAILFeb 12 2025
R-4.5-winOKFeb 12 2025
R-4.5-macOKFeb 12 2025
R-4.5-linuxOKFeb 12 2025
R-4.4-winOKFeb 12 2025
R-4.4-macOKFeb 12 2025
R-4.3-winOKFeb 12 2025
R-4.3-macOKFeb 12 2025

Exports:CombineHittablesCurrent_ICTVExportVirusDataFrameExportVirusGtExportVirusPlotImportVirusTableNew_ICTVSummarizeViralStatsVgConLenViolinVhgAddPhylumVhgBoxplotVhgGetSubjectVhgIdenFacetedScatterPlotVhgIdentityScatterPlotVhgPreprocessTaxaVhgRunsBarplotVhgRunsTableVhgSubsetHittableVhgSumHitsBarplotVhgTabularRasa

Dependencies:AsioHeadersbase64encbigDbitbit64bitopsbslibcachemchromoteclicliprcolorspacecommonmarkcowplotcpp11crayoncurldigestdplyrevaluatefansifarverfastmapfontawesomefsgenericsggplot2gluegtgtablehighrhmshtmltoolshtmlwidgetsisobandjquerylibjsonlitejuicyjuiceknitrlabelinglaterlatticelifecyclemagrittrmarkdownMASSMatrixmemoisemgcvmimemunsellnlmepillarpkgconfigprettyunitsprocessxprogresspromisespspurrrR6rappdirsRColorBrewerRcppreactablereactRreadrrlangrmarkdownsassscalesstringistringrtibbletidyrtidyselecttinytextzdbutf8V8vctrsviridisLitevroomwebsocketwithrxfunxml2yaml

Readme and manuals

Help Manual

Help pageTopics
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 framesExportVirusDataFrame
ExportVirusGt: (Experimental) Export Graphical TablesExportVirusGt
Export Virusparies PlotsExportVirusPlot
Internal function to set default title and cutoff in boxplot functionget_plot_parameters
ImportVirusTable: Import VirusHunterGatherer hittables into RImportVirusTable
New_ICTV: Assign Custom ICTV Data for Use in ViruspariesNew_ICTV
SummarizeViralStats: Generate summary stats outside of plot functionsSummarizeViralStats
VgConLenViolin: Generate a Violinplot of contig length for each group (Gatherer only)VgConLenViolin
VhgAddPhylum: extract Phylum informationVhgAddPhylum
VhgBoxplot: Generate box plots comparing E-values,identity or contig length (Gatherer only) for each virus groupVhgBoxplot
VhgGetSubject: Process and Count Viral Subjects within GroupsVhgGetSubject
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-valueVhgIdentityScatterPlot
VhgPreprocessTaxa: preprocess ViralRefSeq_taxonomy elementsVhgPreprocessTaxa
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 groupVhgRunsTable
VhgSubsetHittable: Filter VirusHunter and VirusGatherer hittablesVhgSubsetHittable
VhgSumHitsBarplot: Generate a bar plot showing the sum of reads/contigs for each virus familyVhgSumHitsBarplot
VhgTabularRasa: Generate Custom Formatted Graphical TablesVhgTabularRasa
Virusparies PackageVirusparies-package Virusparies