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.
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.
To access a stable deployment of the Caenorhabditis RNA-seq Browser Web App, please visit: https://bit.ly/CaenSeq
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')
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 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:
Features of the app include:
The sections below describe the contents of the primary sub-folders within this repository:
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 files for the Shiny app.
User interface files for the Shiny app. Includes custom css and additional README files with methods details.
Static files that can be interactively downloaded within the Caenorhabditis RNA-seq Browser environment.
Utility scripts called by the Shiny app.
Contains pre-processing scripts used to generate the files used in the browser.
This project is licensed under the MIT License.