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vDiveR

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.

Installation

# install vDiveR:
install.packages("vDiveR")

#  Or the development version from GitHub:
# install.packages("devtools")
devtools::install_github("pendy05/vDiveR")

VDiveR Functions Overview

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Version

Install

install.packages('vDiveR')

Monthly Downloads

202

Version

2.0.0

License

MIT + file LICENSE

Maintainer

Pendy Tok

Last Published

September 13th, 2024

Functions in vDiveR (2.0.0)

concat_conserved_kmer

k-mer sequences concatenation
plot_dynamics_proteome

Dynamics of Diversity Motifs (Proteome) Plot
plot_entropy

Entropy plot
plot_dynamics_protein

Dynamics of Diversity Motifs (Protein) Plot
JSON_sample

DiMA (v5.0.9) JSON Output File
plot_correlation

Entropy and total variant incidence correlation plot
plot_conservationLevel

Conservation Levels Distribution Plot
extract_from_NCBI

Extract metadata via fasta file from ncbi
metadata_extraction

Metadata Extraction from NCBI/GISAID EpiCoV FASTA file
extract_from_GISAID

Extract metadata via fasta file from GISAID
json2csv

JSON2CSV
plot_time

Time Distribution of Sequences Plot
plot_worldmap

Geographical Distribution of Sequences Plot
vDiveR-package

vDiveR: Visualization of Viral Protein Sequence Diversity Dynamics
protein_2hosts

DiMA (v5.0.9) JSON converted-CSV Output Sample 2
metadata

Metadata Input Sample
proteins_1host

DiMA (v5.0.9) JSON converted-CSV Output Sample 1