The Caenorhabditis RNA-seq Browser

Web-based Shiny App for browsing and on-demand analysis of Caenorhabditis RNA-seq data originally published as part of the modENCODE project or by the Waterston Lab at the University of Washington (Gerstein et al 2010, Gerstein et al 2014, Boeck et al., 2016, and Warner et al 2019).

This app is based on the Strongyloides RNA-seq Browser. For more information, please see the G3 paper associated with the original project.

Table of Contents

1. General Information
2. App Setup & Deployment
3. App Features
4. Repository Structure
5. Sources
6. License
7. Authors

1. General Information

This repository contains source code for the web-based Caenorhabditis RNA-seq Browser. This app is deployed via Shinyapps.io but can also be run locally. See App Setup and App Features sections below for additional details.

2. App Setup & Deployment

Shinyapps.io version:

To access a stable deployment of the Caenorhabditis RNA-seq Browser Web App, please visit: https://bit.ly/CaenSeq

Running a local copy:

To run the latest version locally from GitHub, use the following command in R/RStudio:
library(shiny)
shiny::runGitHub(repo = 'Caenorhabditis_RNAseq_Browser', username = 'BryantLabUW')

To run a specific release locally use the following commands in R/RStudio:

• For PCs --
  library(shiny)
shiny::runUrl('https://github.com/BryantLabUW/Caenorhabditis_RNAseq_Browser/archive/<RELEASE_VERSION>.zip')

• For Macs --
  library(shiny)
shiny::runUrl('https://github.com/BryantLabUW/Caenorhabditis_RNAseq_Browser/archive/<RELEASE_VERSION>.tar.gz')

Installation notes:

• The script installpackages.R contains commands for installing necessary packages. We recommend running the contents of this file before attempting to run a local version of the browser.
• The download step for runURL/runGitHub takes a substantial amount of time. We recommend downloading this archive and running the application locally.

3. App Features

The Caenorhabditis RNA-seq Shiny Browser enables users to browse Caenorhabditis bulk RNA-seq datasets generated as part of the modENCODE project and perform on-demand analyses including differential expression and gene set enrichment. Data from the following species are currently included: C. elegans, C. briggsae, C. brenneri, C. japonica, and C. remanei. The app permits browsing RNA-seq data in two modes:

1. Browse by Life Stage Mode
2. Browse by Gene Mode

Features of the app include:

• Search for gene(s) of interest using stable geneIDs, gene names, or keywords
• Extract gene expression values for genes of interest
  • Display gene expression across life stages as a heatmap (all genes of interest) or a boxplot (individual genes)
  • Display gene expression across life stages for individual genes and their known Caenorhabditis homologs
  • Download log2 counts per million expression for genes of interest as .xslx
• On demand limma-voom-based pairwise differential gene expression analysis
  • Display results as interactive volcano plots and data tables
  • Download results as .pdf (plots) or .xlsx (datatables)
• Download raw/pre-processed data using user-friendly dropdown menu
  • Study design files (.csv)
  • Log2 counts per million expression for all genes and all samples (.csv)
  • DGEList object (R object; primary data input for the app)

4. Repository Structure

The sections below describe the contents of the primary sub-folders within this repository:

Data

This folder contains pre-processed data files, including study design files, gene annotations, and digital gene expression lists (DGEList) containing filtered and TMM-normalized RNA-seq data. For some species, data is also variance-stabilized (see preprocessing files).

Server

Server files for the Shiny app.

UI

User interface files for the Shiny app. Includes custom css and additional README files with methods details.

www

Static files that can be interactively downloaded within the Caenorhabditis RNA-seq Browser environment.

Utils

Utility scripts called by the Shiny app.

Preprocessing

Contains pre-processing scripts used to generate the files used in the browser.

5. Sources

• Caenorhabditis RNA-seq datasets:
  • Gerstein et al 2010
  • Gerstein et al 2014
  • Boeck et al., 2016
  • Warner et al 2019
• WormBase ParaSite - Gene annotations
• WormBase
• DIYTranscriptomics
• Shiny
• limma

6. License

This project is licensed under the MIT License.

7. Authors

• Astra Bryant, PhD
• Damia Akimori (Hallem Lab, UCLA)
• LaDeana Hillier (Waterston Lab, UW)