FungiExpresZ - 2020 Shiny Contest Submission

FungiExpresZ

Authors: Chirag Parsania, Pooja Sethiya, Koon Ho Wong
Working with Shiny for 1+ years

Abstract: FungiExpresZ is a web-based platform to analyze and visualize user uploaded gene expression data with or without integration of publicly available NCBI-SRA fungal data.

Full Description: FungiExpresZ is a browser-based user interface for analyzing and visualizing gene expression data.

It allows users to visualize their own data as well as more than 13,000 preprocessed SRA gene expression data from 8 different fungal species.

Users can even merge their data with SRA data for integrated analysis and visualization.

Just uploading the matrix of gene expression (.txt file where rows are genes and column are samples), users can generate 12 different data exploration visualizations and 6 different gene ontology (GO) visualizations.

Optionally, users can upload meta data such as gene group and/or sample group to create more complex visualizations such as comparisons of multiple gene groups or sample groups or both in a single graphical device.

In addition, FungiExpresZ supports GO analysis for over 100 different species of fungi. Users can directly pick a set of genes from a scatter plot, line plot or heatmap and pass them on to GO enrichment followed by GO visualizations.

Application use case with demo data can be found under tab About — > Overview at https://cparsania.shinyapps.io/FungiExpresZ/

Data exploration visualizations

  1. Scatter Plot
  2. Multi-Scatter Plot
  3. Corr Heat Box
  4. Density Plot
  5. Histogram
  6. Joy Plot
  7. Box Plot
  8. Violin Plot
  9. Bar Plot
  10. PCA Plot
  11. Line Plot
  12. Heatmap

GO visualizations

  1. Emap plot
  2. Cnet plot
  3. Dot plot
  4. Bar plot
  5. Heat plot
  6. Upset plot

Category: Research
Keywords: bioinformatics, gene expression, data visualization, fungi, NCBI-SRA
Shiny app: https://cparsania.shinyapps.io/FungiExpresZ/
Repo: https://github.com/cparsania/FungiExpresZ
RStudio Cloud: https://rstudio.cloud/project/941624

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