Aneuvis - 2020 Shiny Contest Submission

Aneuvis

Authors: Daniel Piqué
Working with Shiny for 1+ years

Abstract: Aneuvis is a Shiny web application that allows users to determine whether numerical chromosomal variation (NCV), a hallmark of cancer cells, exists between experimental treatment groups. Aneuvis accepts single cell data in a cell-by-chromosome matrix format and automatically generates visualizations and summary statistics that reflect the degree of NCV. Aneuvis is the first user-friendly web application to help researchers identify the genetic and environmental perturbations that promote NCV.

Full Description:Full Description:

aneuvis is a web-based tool to automatically analyze numerical chromosomal variation in single cells.

A 6 minute video tutorial demonstrating the usage of aneuvis is available.

A manuscript describing the app was published in BMC Bioinformatics (Piqué et al 2019) and contains details about the app along with a worked example.

Input and output

Input: The aneuvis workflow begins with the upload of one of three types of single cell chromosomal data (sc-WGS, FISH, or SKY) via a graphical user interface (schematized in panels a-b)

Output: Upon clicking the submit button, aneuvis automatically generates output that is divided into three sections -- table summary, visualization, and hypothesis testing -- that are listed along the navigation bar within aneuvis (schematized in panels a-b).

  • The table summary section quantifies the degree of chromosomal variability per experimental group using six different literature-derived statistics (see Table 1 for a description of the statistics).

  • The visualization section used the statistics shown in table summary, aneuvis automatically generates visualizations that compare experimental groups and that are data type-specific.

  • The hypothesis testing section uses permutation testing to ask whether two or more treatment groups are different from each other in terms of their degree of numerical chromosomal variability.


Category: Research
Keywords: Data Visualization, Bioinformatics, Biostatistics, Aneuploidy, Chromosomes
Shiny app: https://dpique.shinyapps.io/aneuvis/
Repo: https://github.com/dpique/aneuvis
RStudio Cloud: https://rstudio.cloud/project/992210

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