DESCRIPTION

Package: StructuRly
Type: Package
Date: 2018-11-10
Title: A novel shiny app to produce comprehensive, detailed and interactive plots for population genetic analysis
Version: 0.1.0
Authors@R: c(
    person("Nicola", "G.", "Criscuolo", role = c("aut", "cre"), 
            email = "nico.criscuolo981@gmail.com"),
    person("Claudia", "Angelini", role = "aut", 
    email = "c.angelini@na.iac.cnr.it"))
Maintainer: Nicola G. Criscuolo <nico.criscuolo981@gmail.com>
Description: Population genetics is essential for the analysis of allele 
  variants and frequencies within a group of individuals. Nowadays, these studies 
  are usually carried out using Bayesian clustering algorithms implemented, for 
  example, in software such as STRUCTURE or ADMIXTURE. However, the graphical outputs 
  of this applications are not fully informative. StructuRly 0.1.0 aims to facilitate 
  the visualization of Bayesian analyses results in an interactive way. It has been 
  implemented in R using the Shiny library and it has a user-friendly interface that 
  is simple and intuitive. The user can import his genetic data, perform a hierarchical 
  cluster analysis based on the most used geometric and binary distance measures, and compare 
  its results with the ones obtained from STRUCTURE or ADMIXTURE. In fact, the user 
  can also import the tables obtained after an analysis with these softwares, 
  then visualize and personalize the barplot that shows the admixture index (q) 
  of each sample to every cluster. In addition to being able to zoom and edit 
  the graph, display information by passing the cursor on the samples, the real 
  novelty introduced by StructuRly is the ability to (i) visualize the labels of 
  each sample and (ii) group every label according to the user's initial population, 
  thus obtaining an immediate visual feedback compared to the results obtained from 
  the Bayesian analysis. With StructuRly it is also possible to produce the triangle 
  plot useful for showing more specifically the degree of belonging of a sample to 
  a certain cluster. The charts are interactive and can be downloaded in different 
  formats. 
License: GPL-2 | file LICENSE
Encoding: UTF-8
LazyData: TRUE
Imports:
  ggplot2 (>= 3.1.0)
Depends: 
  R (>= 3.5),
  ade4 (>= 1.7),
  adegenet (>= 2.1.1),
  assertthat (>= 0.2.1),
  colourpicker (>= 1.0),
  dendextend (>= 1.12),
  DT (>= 0.9),
  grDevices (>= 3.6.0),
  janitor (>= 1.2.0),
  mcclust (>= 1.0),
  pegas (>= 0.11),
  plotly (>= 4.9.0),
  poppr (>= 2.8.3),
  processx (>= 3.4.1),
  randomcoloR (>= 1.1.0),
  RColorBrewer (>= 1.1),
  reshape2 (>= 1.4.3),
  scales (>= 1.0.0),
  shiny (>= 1.3.2),
  shinymeta (>= 0.2.0),
  shinyjs (>= 1.0),
  tidyr (>= 1.0.0)
Repository: GitHub
RoxygenNote: 6.1.1
URL: https://github.com/nicocriscuolo/StructuRly
BugReports: https://github.com/nicocriscuolo/StructuRly/issues