Package: vivaldi 1.0.1

David Gresham

vivaldi: Viral Variant Location and Diversity

Analysis of minor alleles in Illumina sequencing data of viral genomes. Functions in 'vivaldi' primarily operate on vcf files.

Authors:Marissa Knoll [aut], Katherine Johnson [aut], Megan Hockman [aut], Eric Borenstein [aut], Mohammed Khalfan [aut], Elodie Ghedin [aut], David Gresham [aut, cre, cph]

vivaldi_1.0.1.tar.gz
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vivaldi.pdf |vivaldi.html✨
vivaldi/json (API)

# Install 'vivaldi' in R:

install.packages('vivaldi', repos = c('https://greshamlab.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/greshamlab/vivaldi/issues

Datasets:

example_filtered_SNV_df - Example Dataframe The DF_filt_SNVs dataframe created in the vignette

On CRAN:

4.78 score 3 stars 6 scripts 183 downloads 20 exports 83 dependencies

Last updated 9 months agofrom:dcc628ac3f. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 12 2024
R-4.5-win	OK	Nov 12 2024
R-4.5-linux	OK	Nov 12 2024
R-4.4-win	OK	Nov 12 2024
R-4.4-mac	OK	Nov 12 2024
R-4.3-win	OK	Nov 12 2024
R-4.3-mac	OK	Nov 12 2024

Exports:add_metadata af_distribution arrange_data dNdS_segment filter_variants merge_replicates plot_shannon position_allele_freq prepare_annotations read_reference_fasta_dna shannon_entropy shared_snv_plot shared_snv_table snpeff_info snv_genome snv_location snv_segment tally_it tstv_plot tstv_ratio

Dependencies:ade4 ape askpass base64enc bslib cachem cli cluster colorspace cpp11 crosstalk curl data.table digest dplyr evaluate fansi farver fastmap fontawesome fs generics ggplot2 glue gtable highr htmltools htmlwidgets httr isoband jquerylib jsonlite knitr labeling later lattice lazyeval lifecycle magrittr MASS Matrix memoise memuse mgcv mime munsell nlme openssl permute pillar pinfsc50 pixmap pkgconfig plotly promises purrr R6 rappdirs RColorBrewer Rcpp RcppArmadillo rlang rmarkdown sass scales segmented seqinr sp stringi stringr sys tibble tidyr tidyselect tinytex utf8 vcfR vctrs vegan viridisLite withr xfun yaml

Vivaldi vignette

Rendered fromvignette.Rmdusingknitr::rmarkdownon Nov 12 2024.

Last update: 2023-03-02
Started: 2022-10-07

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
add_metadata	add_metadata
af_distribution	af_distribution
arrange_data	arrange_data
dNdS_segment	dNdS_segment
Example Dataframe The DF_filt_SNVs dataframe created in the vignette	example_filtered_SNV_df
filter_variants	filter_variants
merge_replicates	merge_replicates
plot_shannon	plot_shannon
position_allele_freq	position_allele_freq
prepare_annotations	prepare_annotations
read_reference_fasta_dna	read_reference_fasta_dna
shannon_entropy	shannon_entropy
shared_snv_plot	shared_snv_plot
shared_snv_table	shared_snv_table
snpeff_info	snpeff_info
snv_genome	snv_genome
snv_location	snv_location
snv_segment	snv_segment
tally_it	tally_it
tstv_plot	tstv_plot
tstv_ratio	tstv_ratio