Package: vDiveR 2.0.1

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:Pendy Tok [aut, cre], Li Chuin Chong [aut], Evgenia Chikina [aut], Yin Cheng Chen [aut], Mohammad Asif Khan [aut]

vDiveR_2.0.1.tar.gz
vDiveR_2.0.1.zip(r-4.5)vDiveR_2.0.1.zip(r-4.4)vDiveR_2.0.1.zip(r-4.3)
vDiveR_2.0.1.tgz(r-4.5-any)vDiveR_2.0.1.tgz(r-4.4-any)vDiveR_2.0.1.tgz(r-4.3-any)
vDiveR_2.0.1.tar.gz(r-4.5-noble)vDiveR_2.0.1.tar.gz(r-4.4-noble)
vDiveR_2.0.1.tgz(r-4.4-emscripten)vDiveR_2.0.1.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

Datasets:

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

On CRAN:

conservation-level diversity entropy sequences viral visualization

3.78 score 4 scripts 295 downloads 10 exports 91 dependencies

Last updated 1 months agofrom:b863a8043d. Checks:1 OK, 7 NOTE. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Mar 02 2025
R-4.5-win	NOTE	Mar 02 2025
R-4.5-mac	NOTE	Mar 02 2025
R-4.5-linux	NOTE	Mar 02 2025
R-4.4-win	NOTE	Mar 02 2025
R-4.4-mac	NOTE	Mar 02 2025
R-4.3-win	NOTE	Mar 02 2025
R-4.3-mac	NOTE	Mar 02 2025

Exports:concat_conserved_kmer json2csv metadata_extraction plot_conservation_level plot_correlation plot_dynamics_protein plot_dynamics_proteome plot_entropy plot_time plot_world_map

Dependencies:abind askpass backports boot broom car carData cli colorspace commonmark corrplot cowplot cpp11 curl Deriv doBy dplyr fansi farver Formula generics gghalves ggplot2 ggpubr ggrepel ggsci ggsignif ggtext glue gridExtra gridtext gtable httr isoband jpeg jsonlite labeling lattice lifecycle lme4 magrittr maps markdown MASS Matrix MatrixModels mgcv microbenchmark mime minqa modelr munsell nlme nloptr nnet numDeriv openssl pbkrtest pillar pkgconfig png polynom purrr quantreg R6 rbibutils RColorBrewer Rcpp RcppEigen Rdpack reformulas rentrez rlang rstatix scales SparseM stringdist stringi stringr survival sys tibble tidyr tidyselect utf8 vctrs viridisLite withr xfun XML xml2

Citation

Development and contributors

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 (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