Package: vDiveR 2.2.1
Pendy Tok
vDiveR: Visualization of Viral Protein Sequence Diversity Dynamics
To ease the visualization of outputs from Diversity Motif Analyser ('DiMA'; <https://github.com/BVU-BILSAB/DiMA>). 'vDiveR' allows visualization of the diversity motifs (index and its variants – major, minor and unique) for elucidation of the underlying inherent dynamics. Please refer <https://vdiver-manual.readthedocs.io/en/latest/> for more information.
Authors:
vDiveR_2.2.1.tar.gz
vDiveR_2.2.1.zip(r-4.7-any)
vDiveR_2.2.1.tar.gz(r-4.7-any)vDiveR_2.2.1.tar.gz(r-4.6-any)
vDiveR_2.2.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
vDiveR/json (API)
| # Install 'vDiveR' in R: |
| install.packages('vDiveR', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
- JSON_sample - DiMA (v5.0.9) JSON Output File
- metadata - Metadata Input Sample
- protein_2hosts - DiMA (v5.0.9) JSON converted-CSV Output Sample 2
- proteins_1host - DiMA (v5.0.9) JSON converted-CSV Output Sample 1
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:9194d9d2da. Checks:5 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 199 | ||
| source / vignettes | OK | 265 | ||
| linux-release-x86_64 | OK | 178 | ||
| windows-devel-x86_64 | OK | 103 | ||
| wasm-release | OK | 144 |
Exports:concat_conserved_kmerjson2csvmetadata_extractionplot_conservation_levelplot_correlationplot_dynamics_proteinplot_dynamics_proteomeplot_entropyplot_timeplot_world_map
Dependencies:abindaskpassbackportsbootbroomcarcarDataclicolorspacecommonmarkcorrplotcowplotcpp11curlDerivdoBydplyrfarverforecastFormulafracdiffgenericsggplot2ggpubrggrepelggsciggsignifggtextgluegridExtragridtextgtablehttrisobandjpegjsonlitelabelinglatticelifecyclelitedownlme4lmtestmagrittrmapsmarkdownMASSMatrixMatrixModelsmgcvmimeminqamodelrnlmenloptrnnetnumDerivopensslpatchworkpbkrtestpillarpkgconfigpngpolynompurrrquantregR6rbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreformulasrentrezrlangrstatixS7scalesSparseMstringdiststringistringrsurvivalsystibbletidyrtidyselecttimeDateurcautf8vctrsviridisLitewithrxfunXMLxml2zoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| k-mer sequences concatenation | concat_conserved_kmer |
| Extract metadata via fasta file from GISAID | extract_from_GISAID |
| Extract metadata via fasta file from ncbi | extract_from_NCBI |
| DiMA (v5.0.9) JSON Output File | JSON_sample |
| JSON2CSV | json2csv |
| Map data region to ggplot2 region | match_region_to_target |
| Metadata Input Sample | metadata |
| Metadata Extraction from NCBI/GISAID (EpiFlu/EpiCoV/EpiPox/EpiArbo) FASTA file | metadata_extraction |
| Conservation Levels Distribution Plot | plot_conservation_level |
| Entropy and total variant incidence correlation plot | plot_correlation |
| Dynamics of Diversity Motifs (Protein) Plot | plot_dynamics_protein |
| Dynamics of Diversity Motifs (Proteome) Plot | plot_dynamics_proteome |
| Entropy plot | plot_entropy |
| Time Distribution of Sequences Plot | plot_time |
| Geographical Distribution of Sequences Plot | plot_world_map |
| DiMA (v5.0.9) JSON converted-CSV Output Sample 2 | protein_2hosts |
| DiMA (v5.0.9) JSON converted-CSV Output Sample 1 | proteins_1host |
