Introduction

CONTENTO

CONTrast ExploratioN Toolkit for Omics!

Documentation

Full documentation, including tutorials for creating SE and annotation files, is available at: https://klemonlab.github.io/CONTENTO/

Running CONTENTO

CONTENTO can be run in two ways. We recommend the container, since it ships with R, Bioconductor, and every dependency pre-installed, and behaves identically on any operating system.

Option 1: Run the container (recommended)

A container bundles the app together with everything it needs to run. You only need to install a container runtime once:

• macOS and Windows: Podman Desktop, free and open source. Docker Desktop also works, but requires a paid subscription at larger organizations (more than 250 employees or more than $10 million in annual revenue), which usually includes universities and hospitals.
• Linux: Docker Engine or Podman, both free and available from your distribution’s package manager.

Then start CONTENTO from a terminal (with Podman Desktop running):

podman run --rm -p 3838:3838 ghcr.io/klemonlab/contento:latest

If you use Docker, replace podman with docker; the rest of the command is identical. The first run downloads the image, which takes a few minutes. When the terminal shows Listening on http://0.0.0.0:3838, open your web browser and navigate to:

http://localhost:3838

Press Ctrl+C in the terminal to stop the app.

Loading your data. Upload your SE file in the app’s sidebar, and an annotation file from the load panel if needed. Built-in annotations are included in the container and load automatically when metadata(se)$annotation names one of them. Uploaded files are only kept for the current session.

Trying CONTENTO with example data. The example SE files are not included in the container. Download them from inst/extdata/SE and upload them in the sidebar. See Create SE for CONTENTO for how they were built.

Using your own annotation files. To load your own annotation files automatically instead of uploading them each session, mount the folder that contains them and point CONTENTO_ANNOTATION_DIR to it:

podman run --rm -p 3838:3838 \
    -v /path/to/annotations:/annotations:ro \
    -e CONTENTO_ANNOTATION_DIR=/annotations \
    ghcr.io/klemonlab/contento:latest

Pinning a version. latest always points to the newest release. For analyses you intend to publish, replace latest with a specific release version (see Releases) and report that version in your methods:

podman run --rm -p 3838:3838 ghcr.io/klemonlab/contento:0.2.0

Building the image yourself. A Dockerfile is included in the repository, so you can build and run the image locally from the cloned repository:

podman build -t contento .
podman run --rm -p 3838:3838 contento

Option 2: Run locally within R/RStudio

Some users may prefer to execute CONTENTO directly from an existing R installation, usually used in conjunction with the popular IDE RStudio.

Clone the CONTENTO repository:

git clone https://github.com/klemonlab/contento.git

After opening the project (CONTENTO.Rproj) within Rstudio, install the dependencies by running:

install.packages(c(
    "shiny",
    "shinydashboard",
    "shinycssloaders",
    "DT",
    "plotly",
    "tidyverse",
    "purrr",
    "viridis",
    "RColorBrewer",
    "ComplexUpset",
    "scales",
    "ggiraph",
    "gridExtra",
    "patchwork"
))

if (!requireNamespace("BiocManager"))
    install.packages("BiocManager")

BiocManager::install(c(
    "ComplexHeatmap",
    "DESeq2",
    "fgsea",
    "msigdbr",
    "circlize",
    "SummarizedExperiment"
))

Open app.R in RStudio and click the interactive :arrow_forward: Run App button, or execute:

shiny::runApp("app.R")

The application will then become available in your web browser.

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Citation

If you use this application in scientific work, please cite:

Isabel FE, et al. “CONTENTO: CONTrast ExploratioN Toolkit for Omics”. https://github.com/KLemonLab/CONTENTO

DOI: https://doi.org/10.5281/zenodo.21629492

This DOI always resolves to the latest release; the DOI for each specific version is listed on the Zenodo page.

License

This project is covered under the GPL-3 license.

Contact

Issues, bug reports, and feature requests are welcome through the GitHub issue tracker.