Asc-Seurat - Analytical single-cell Seurat-based web application (v2.2)

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.

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

Realese notes

• v2.2 - Release 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.

Asc-Seurat - Analytical single-cell Seurat-based web application (v2.1)

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.

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

Realese notes

• 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.

Asc-Seurat - Analytical single-cell Seurat-based web application

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.

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

Release notes

• 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.

Asc-Seurat - Analytical single-cell Seurat-based web application

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.

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