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.
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.
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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 While the docker version of Asc-Seurat is stable, it may become outdated as the packages on wich it relies on are updated.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.
v2.0 - Released on May 19th, 2021.
v1.0 - Released on March 19th, 2021.
Download Asc-Seurat's docker image.
# Download the docker image:
docker pull kirstlab/asc_seurat
# 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
:heavy_check_mark: Then, open your preferred web browser and paste the address http://localhost:3838/
Please, visit https://asc-seurat.readthedocs.io/en/latest/ for a complete documentation.
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.
Distributed under the GNU General Public License v3.0. See LICENSE
for more information.