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License: GPL v3 readthedocs DOI

Asc-Seurat

Analytical single-cell Seurat-based web application


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About Asc-Seurat

Asc-Seurat (Analytical single-cell Seurat-based web application) is a web application based on Shiny. Pronounced as “ask Seurat”, it provides a click-based, easy-to-install, and easy-to-use interface that allows the execution of all steps necessary for scRNA-seq analysis. It integrates many of the capabilities of the Seurat and Dynverse and also allows an instantaneous functional annotation of genes of interest using BioMart.

Asc-Seurat workflow overview.

Prerequisites

To install Asc-Seurat, you need to have Docker installed on your machine. Docker needs to be properly installed and configured in the user's machine. Check the installation instructions provided by Docker at https://docs.docker.com/engine/install.

Release notes

⚠️ WARNING
Please be aware that Asc-Seurat uses multiple R packages and that many of those are in continuous development. While the docker version of Asc-Seurat is stable, it may become outdated as the packages on wich it relies on are updated. Here you can find a list of the packages used by Asc-Seurat and their versions.

  • v2.2 - Released on February 8th, 2022

    • Add the capacity to load a clustered dataset in the tab for the individual sample analysis.

    • Add the capacity to load a clustered dataset in the tab for the integrated sample analysis.

    • Genes identified as mitochondrial genes via the regex expression are now shown to the users.

    • Changes the color scheme of the dynverse's plots to match the color scheme used by Seurat's plots.

    • Small changes in the interface to improve usability.

    • Fix a bug in the download of markers identified for multiple clusters in the integrated dataset. If a gene was identified as a marker in multiple clusters, a number was appended in the gene's name.

    • Fix a bug that caused the app to crash when searching for conserved markers in an integrated dataset, and the gene was not expressed in one or more of the samples.

    • Fix a bug where plots were exported with a dark background.

    • Fix a bug in the advanced plots that caused expressed genes not to be identified. When using integrated datasets, the function now looks for the RNA assay instead of the integrated assay.

    • Fix a bug where the app would crash when downloading the plots generated in the trajectory inference tab.

  • v2.1 - Released on May 26th, 2021.

    • Changes the assay used for differential expression analysis and visualization to "RNA" when using SCTransform normalization. Therefore, "SCT" assay is used for the steps until clustering the data.
    • Changes the output of the differential expression analysis to the format required for the visualization tools.

  • v2.0 - Released on May 19th, 2021.

    • Inclusion of SCTransform normalization
    • Addition of stacked violin plots
    • Addition of multiple-genes dot plot
    • Improvements on the user interface
    • Improvements in the app stability
    • Fix of minor bugs.

  • v1.0 - Released on March 19th, 2021.

    • Release of Asc-Seurat.

Installation

Download Asc-Seurat's docker image.

 # Download the docker image:
 docker pull kirstlab/asc_seurat

Quickstart

# Starts Asc-Seurat on MacOS or Linux
docker run -v $(pwd):/app/user_work -v /var/run/docker.sock:/var/run/docker.sock -d --name Asc_Seurat --rm -p 3838:3838 kirstlab/asc_seurat

# Starts Asc-Seurat using Windows CMD
docker run -v %cd%:/app/user_work -v /var/run/docker.sock:/var/run/docker.sock -d --name Asc_Seurat --rm -p 3838:3838 kirstlab/asc_seurat

# Starts Asc-Seurat using Windows Powershell
docker run -v ${PWD}:/app/user_work -v /var/run/docker.sock:/var/run/docker.sock -d --name Asc_Seurat --rm -p 3838:3838 kirstlab/asc_seurat

✔️ Then, open your preferred web browser and paste the address http://localhost:3838/

Usage

Please, visit https://asc-seurat.readthedocs.io/en/latest/ for a complete documentation.

Reference

Pereira WJ, Almeida FM, Balmant KM, Rodriguez DC, Triozzi PM, Schmidt HW, Dervinis C, Pappas Jr. GJ, Kirst M. Asc‑Seurat: analytical single‑cell Seurat‑based web application. BMC Bioinformatics 22, 556 (2021).

Pereira WJ, Almeida FM, Balmant KM, Rodriguez DC, Triozzi PM, Schmidt HW, Dervinis C, Pappas Jr. GJ, Kirst M. Asc-Seurat – Analytical single-cell Seurat-based web application. biorxiv, 2021.

License

Distributed under the GNU General Public License v3.0. See LICENSE for more information.