Sequncing data analysis and plots Shiny app

This app takes DeepTools matrix files of DNAseq and RNAseq data to make publication ready plots

Features

• Create line plots, quickly and easily changing ascetics
• Explore and create genes lists from data
• Load gene lists or use generated to make plots of subsets of genes

Prerequisites

• R (version 4.4 or higher)
• RStudio
• computeMatrix files from DeepTools (one sample per file)

Required Packages

install.packages(c(
    "tidyverse",
    "shiny",
    "shinydashboard",
    "shinydashboardPlus",
    "shinycssloaders",
    "shinyWidgets",
    "shinyjs",
    "RColorBrewer",
    "colourpicker",
    "colorspace",
    "DT",
    "patchwork",
    "zip",
    "ggpubr",
    "ggtext",
    "fastcluster",
    "dendextend",
    "valr"
  ))

Running the App Locally

1. Open RStudio, from the File menu select "New Project", -> "Version Control", -> "GIT"
   https://github.com/BBerickson/Bentools_V9.git

2. paste URL 'https://github.com/BBerickson/Bentools_V9.git', set project name and location -> Create

3. Run the app:

shiny::runApp()

Or in RStudio, open Ben_tools.v9.R and click the "Run App" button.

Usage Guide

Loading Test Data

The app includes sample test files for demonstration:

1. Click the Browse button
2. Navigate to the test_files/ folder
3. Select one of the example .matrix.gz files or for batch loading with meta data select matrix.url.txt

Generating Plots

After loading data:

1. Plot tab in sidebar will light up, select

2. A popup will give options for plot labels, defaults to info in the Matrix header
3. Click SET and Plot

Example Output

Here's an example of the visualization output:

Use drop down to select which sample to plot, (genes in common will be plotted of active samples within a drop down list)

Set ascetics drop down

Apply different functions on the plots

Example Tool Usage, Filter Sum

1. Select the filter tool tab

2. Select bin range, and sample(s) to use

3. Click filter sum

A preview plot will be generated along with a count of the number of genes that passed filter. Switch back to the main plots tab to see the newly generated gene list

1. Deselect / Select samples to plot

2. Click Update Plot

Contact

Benjamin Erickson - BBerickson@gmail.com

Project Link: https://github.com/BBerickson/Bentools_V9.git