This repository contains the R package. To see an example of how to create an OmicNavigator study, check out the repository OmicNavigatorExample. If you're a developer interested in the web application code, check out the repository OmicNavigatorWebApp.
- Simple, yet flexible study-model-test data model for differential and/or enrichment analyses
- Well documented data-in functions and a novel data container
- User-defined results and feature plots
- Richly featured tables
- Interactive scatter/volcano plots
- Interactive barcode plots for enrichment results
- Dynamic network views of enriched terms
- Multi-set filtering across hypothesis tests
To get a quick sense of how the app works, the quick start instructions below install the package, create a very minimal study, and then starts the app. It should automatically open a new tab in your browser. When you're done, press ctrl+c or Esc to stop running the app.
# Install and load the package install.packages("OmicNavigator", dependencies = TRUE) library(OmicNavigator) # Create a very minimal study with a single results table quickstart <- createStudy("quickstart") data("RNAseq123") head(basal.vs.lp) resultsTable <- basal.vs.lp[, -2:-3] quickstart <- addResults(quickstart, list(model = list(test = resultsTable))) installStudy(quickstart) # (optional) Install the example study RNAseq123 which demos many of the app's # available features install.packages(c("gplots", "heatmaply", "iheatmapr", "plotly", "viridis")) tarball <- "https://github.com/abbvie-external/OmicNavigatorExample/releases/latest/download/ONstudyRNAseq123.tar.gz" install.packages(tarball, repos = NULL) # Install and start the web app installApp() startApp()
To learn how to add your own data to the app, please read the User's Guide attached to the latest GitHub Release. The more data you add, the more features are automatically enabled in the app (e.g. the Enrichment Analysis tab is available once you add the results of an enrichment analysis).
OmicNavigator is a web app and R code bundled together as an R package. You can install OmicNavigator multiple ways.
This is the quickest and easiest method for you to be able to install OmicNavigator and run the web app on your local machine.
Install the OmicNavigator R package directly from CRAN:
install.packages("OmicNavigator", dependencies = TRUE)
Install the web app:
Alternatively, you can install the OmicNavigator release tarball, which already includes the web app bundled with the R package.
Download the tarball from the latest GitHub Release. It will look like
x.x.xcorresponds to the version.
Install the dependencies:
remotes::install_deps("OmicNavigator_x.x.x.tar.gz", dependencies = TRUE)
Install OmicNavigator from the release tarball:
In the R console:
install.packages("OmicNavigator_x.x.x.tar.gz", repos = NULL)
In the terminal:
R CMD INSTALL --no-multiarch --with-keep.source OmicNavigator_x.x.x.tar.gz
If you are only using the R package functions, and don't need to run the app, you can perform a minimal installation. This is useful if you are using OmicNavigator in a data engineering pipeline or as part of a continuous integration build.
Install the OmicNavigator R package directly from CRAN, without the extra dependencies required to run the app:
If you need access to the latest changes to OmicNavigator, you can install the development version of the package directly from GitHub.
Install the OmicNavigator R package directly from GitHub:
remotes::install_github("abbvie-external/OmicNavigator", dependencies = TRUE)
Install the web app:
Some of the R package dependencies require external software libraries to already be installed on your machine (e.g. the R package curl requires the system library libcurl). Unfortunately R is unable to install these for you automatically. If you are using Linux/macOS, you will need to install these system libraries yourself first.
If you are using Debian/Ubuntu, you can install all of the required system libraries using the commands below:
sudo apt update sudo apt install \ libcurl4-openssl-dev \ libssl-dev \ libprotobuf-dev \ protobuf-compiler \ libxml2-dev
Here is a table of the known system dependencies that you will need to install.
|R package||System library||Operating system||Installation|
OmicNavigator is deployed as an OpenCPU app. The OpenCPU system enables embedded scientific computing with R.
OmicNavigator development is influenced by many existing bioinformatics and data visualization tools, including the set analysis visualization tool UpSet and the enrichment analysis network visualization tool EnrichmentMap
Please note that the OmicNavigator project is released with guidelines on how to best contribute and a code of conduct.
You can find these documents in