DESCRIPTION

Package: herpesdrg
Type: Package
Title: human Herpesviridae Drug Resistance Genotyping
Version: 0.2
Authors@R: c(
    person("OJ", "Charles", email = "oscar.charles.18@ucl.ac.uk", role = c("aut", "cre")))
Maintainer: Charles OJ <oscar.charles.18@ucl.ac.uk>
Description: Resistance Genotyping tool for HCMV HSV1 HSV2 VZV HHV6b sequencing data, a command line, website and database.
    The package includes
    Database: Simple Resistance or Polymorphism against a gene, mutation & drug.
    Shiny app: An intuitive way for scientists to call resitance on their data. Includes a clinical overview of the resistance phenotype, as well as some plots that may be of interest.
    Functions: Users happy running R code or using the terminal, can ofcourse interact with the packages functionality. This will return the resistance dataframes without any of the plotting or overviews. It's the same back end as the shiny app.
    Cite: Please cite us in your work, if you used this tool or database.
License: MIT + file LICENSE
Encoding: UTF-8
biocViews:
Depends:
  R (>= 3.5.0),
	shiny
Imports:
	  VariantAnnotation,
    ggplot2,
    stringr,
    DT (>= 0.5),
    reshape2,
    Biostrings,
    dplyr,
    IRanges,
    GenomicRanges,
    GenomeInfoDb,
    GenomicFeatures,
    Rsamtools,
    readr,
    ggrepel,
    AnnotationDbi,
    S4Vectors,
    utils,
    rlang,
    magrittr,
    ape
Suggests: 
    knitr,
    rmarkdown,
    testthat
VignetteBuilder: knitr
RoxygenNote: 7.1.2
URL: https://github.com/ojcharles/herpesdg
BugReports: https://github.com/ojcharles/herpesdrg/issues