Package: vDiveR 2.0.0
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_2.0.0.tar.gz
vDiveR_2.0.0.zip(r-4.5)vDiveR_2.0.0.zip(r-4.4)vDiveR_2.0.0.zip(r-4.3)
vDiveR_2.0.0.tgz(r-4.4-any)vDiveR_2.0.0.tgz(r-4.3-any)
vDiveR_2.0.0.tar.gz(r-4.5-noble)vDiveR_2.0.0.tar.gz(r-4.4-noble)
vDiveR_2.0.0.tgz(r-4.4-emscripten)vDiveR_2.0.0.tgz(r-4.3-emscripten)
vDiveR.pdf |vDiveR.html✨
vDiveR/json (API)
NEWS
| # Install 'vDiveR' in R: |
| install.packages('vDiveR', repos = c('https://pendy05.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/pendy05/vdiver/issues
- 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
conservation-leveldiversityentropysequencesviralvisualization
Last updated 2 months agofrom:25f50aaa2d. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 12 2024 |
| R-4.5-win | NOTE | Oct 12 2024 |
| R-4.5-linux | NOTE | Oct 12 2024 |
| R-4.4-win | NOTE | Oct 12 2024 |
| R-4.4-mac | NOTE | Oct 12 2024 |
| R-4.3-win | NOTE | Oct 12 2024 |
| R-4.3-mac | NOTE | Oct 12 2024 |
Exports:concat_conserved_kmerjson2csvmetadata_extractionplot_conservationLevelplot_correlationplot_dynamics_proteinplot_dynamics_proteomeplot_entropyplot_timeplot_worldmap
Dependencies:abindaskpassbackportsbootbroomcarcarDataclicolorspacecommonmarkcorrplotcowplotcpp11curlDerivdoBydplyrfansifarverFormulagenericsgghalvesggplot2ggpubrggrepelggsciggsignifggtextgluegridExtragridtextgtablehttrisobandjpegjsonlitelabelinglatticelifecyclelme4magrittrmapsmarkdownMASSMatrixMatrixModelsmgcvmicrobenchmarkmimeminqamodelrmunsellnlmenloptrnnetnumDerivopensslpbkrtestpillarpkgconfigplyrpngpolynompurrrquantregR6RColorBrewerRcppRcppEigenrentrezrlangrstatixscalesSparseMstringistringrsurvivalsystibbletidyrtidyselectutf8vctrsviridisLitewithrxfunXMLxml2
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 |
| Metadata Input Sample | metadata |
| Metadata Extraction from NCBI/GISAID EpiCoV FASTA file | metadata_extraction |
| Conservation Levels Distribution Plot | plot_conservationLevel |
| 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_worldmap |
| DiMA (v5.0.9) JSON converted-CSV Output Sample 2 | protein_2hosts |
| DiMA (v5.0.9) JSON converted-CSV Output Sample 1 | proteins_1host |
