This document describes a Shiny web application called ShinySRAdb that provides a user-friendly interface for querying, viewing, and interacting with data from the Sequence Read Archive (SRA) database. It was programmed using the Shiny Apps package in R to make functions from the SRAdb package more accessible. The application allows users to search the SRA, filter results, view information on selected records, export results, and perform operations like downloading FASTQ files or visualizing entity relationships.

1. Shiny Web Application for
SRAdb
Olivia Zhang
8/13/2015
Thomas Jefferson High School for Science and
Technology
NCI Summer Intern

2. ShinySRAdb Web application
Overview:
o User interface for SRAdb package
o Programmed using “Shiny Apps” package in R
o Easier way to query, view, and interact with SRA data
Installation:
o Full Instructions and program files at
https://github.com/oliviazz/SRAdb-app
o R commands for usage:
• Install.packages(“devtools”) and library(devtools)
• install_github('seandavi/SRAdb-app’)
• Library(ShinySRAdb)
• ShinySRAdb() to launch

3. Shiny Applications
• R Package for creating Web Applications
• Server.R and Ui.R files
o Server.R file runs R Session
o UI File provides HTML-based user interface
• Dynamic, responsive data outputs
• Shiny App Structure:
o UI file contains design elements, input widgets (text input, checkboxes)
o Server file collects user input through widgets IDs
o Server uses input to return unique output objects (data tables, plots) to the
UI file
Widget in UI
Defining table output in server

4. SRAdb Application Structure
• Workflow Design
o Search Function & Operation Function
o Enter Search Terms > Filter Results > Perform Operations on Results

5. 1) Search Results
• SRAdb function “getSRA” performs full-text search across entire SQLite
database and returns datatable of results
o Compatible with advanced search options, *, “”, OR
• User input for search terms and data type accepted as arguments
o text input (id “searchTerms”) and select input widgets (id “dataType”)
UIServer

6. 2) Filtering Results
• Users may need a way to narrow down results from a broad full text search
o Achieved through DT Package and user input as SRAdb function arguments
Sort results by value of a selected
column (i.e. by most recent date)
Select SRA Data TypeSpecify value for specific column
Search within results

7. 3) DT Package for formatting and filtering:
• DT: R Package for Data Table customization
o Shiny methods masked
• Data table customized using DT Packages’s built-in extensions and options
o Customizations included in Server File when defining tableOutput

8. 4) “Isolate” Functions
Shiny reactive outputs regenerates automatically when dependency inputs change
o Search Results would be regenerated w/ each letter typed
Outputs isolated to save unnecessary function calls
• Only defined inputs trigger responses (i.e. button click)
• ObserveEvent code is also only triggered by a certain event
• Use in App:
o Search Result table not regenerated unless search button pressed
o Operation function not performed unless action button pressed

9. 5) Performing Operations
• Operations performed for selected rows
o Click to select rows
o Choose an operation from dropdown menu
o SRAdb functions that accept accessions as arguments
• Accessions parsed from selected rows (input$tableName_rows_selected)

10. 5) Performing Operations (cont).
• Each choice in input widget returns different string value to server
o Switch statement to perform correct function based on string value
• Related Accession Codes → listSRAFile()
• Export Selected → Download Handler
• Get FASTQ info → getFASTQInfo()
• Get SRA info → getSRAInfo()
• FASTQ Dump → fastqDump()
• Display Entity Graph → sraGraph()

11. 6) Operation Examples
• Get SRA Info
o Accession codes and SRA FTP Download Link, size, upload date
• Get FASTQ Info
o Accession codes and FASTQ FTP Download Link, file size, upload date

12. 6) Operation Examples (cont.)
Display Entity Relationship Graph
o Parses accession from the row
selected
o SRAConvert() used to find all
related accessions
o sraGraph() graphs accessions
appropriately
o Helpful for visualizing data
relationships
Get Related Accession Codes
o Returns the run, experiment,
study, sample, and submission
accessions associated with
selected row

13. 6) Operation Examples (cont.)
• Export Selected Rows
o Used Shiny Download button & handler
• File name: Defined used search terms
entered and date
• Contents: Selected rows of search result
table written into .csv file
• Export Full SRA
o Same process, with full SRA table as file content
(all columns)

14. 6) Operation Examples (cont.)
• FASTQ Dump File
o Implementation of NCBI SRA Toolkit’s ‘FASTQ Dump’ function in R language
o Options panel automatically pops up if “FASTQ Dump” operation chosen
o Download FASTQ files for a specific run
o Specify FASTQ options, output format, download location, and more
• Arguments in “fastqDump()” method

15. 7) Additional Features
• Alerts
o Alerts generated using ShinyBS
Package
o “if Statements” to catch errors
o Prevents data mismatches for
operations, empty result cases, etc.
• Progress Bar
• Indicate if app is loading
• Used Shiny::progress to initiate, closes
on function exit
• Let User know what program is doing

16. Workflow Examples
Find Information on Studies of Human Breast Cancer:
o Search “Breast Cancer”, View -> Study
o Search within results “human”
o Use column selection tool to show only desired data
fields
o Choose selected rows and export as .csv file OR
o Click “Print” button and edit print setup accordingly

17. Workflow Examples
Get FASTQ Files for a run related to Thyroid Cancer:
o Search Studies > “Thyroid Cancer”
o Select a row > “Get related accessions”
o Search run Accession code, data Type = “run”
o Select a Row > “Perform FASTQ Dump”
o Configure FASTQ Options, “Submit”
o Open Download Directory to view file

18. Conclusion
• Web application provides a simple user interface for the
SRAdb package
o Users can query SRA broadly or specifically
o Users can download SRA/FASTQ files, perform FASTQ dumps, view
entity relationship graphs, convert data types, export results, and
more
o SRA usage simplified through Graphic view of SRA and SRAdb
functions
• Application Code at: https://github.com/oliviazz/SRAdb-
app

19. Dr. Sean Davis
Dr. Jack Zhu
Dr. Josh Waterfall
Members of Dr. Meltzer’s Lab
Acknowledgements