Asc-Seurat: Analytical single-cell Seurat-based web application
3.0.6

General information

  • Installation
    • Option 1 — Docker (recommended)
    • Option 2 — R package from GitHub
      • Python dependencies for PAGA
    • Resource notes
    • Verifying the installation
  • Getting started
    • Launching the app
    • The Demo tab
    • Top-level navigation
    • Working with your own data
  • References
    • Analytical core
    • Additional packages
      • CRAN
      • Bioconductor
  • License

Analysis of individual sample

  • Loading the data of an individual sample
    • Loading the data
  • Quality control
    • Filtering mode
    • Doublet removal
    • Downloads
  • Clustering
    • Step 3: Normalization & PCA
    • Choosing PCA dimensions
    • Step 4: Clustering & Visualization
    • Renaming clusters
    • Selecting clusters of interest
  • Markers identification and differential expression analysis
  • Expression visualization
    • Gene sources
    • Expression values
    • Plots

Analysis of multiple samples

  • Loading the data and integration of multiple samples
    • Declaring the samples
    • Setting per-sample QC parameters
    • Choosing the integration method
    • Saving the integrated object for reuse
  • Integrated quality control
  • Clustering
    • Integration QC and PCA dimensions
    • Step 2: Clustering & Visualization
    • Integrated UMAP summaries
    • Cells per cluster and subsetting
  • Markers identification and differential expression analysis
    • Analysis modes
    • Marker table
  • Integrated expression visualization
    • Gene sources
    • Expression values
    • Plots

Trajectory inference

  • Trajectory inference
    • Running trajectory inference
    • Trajectory gene discovery
    • Installing the Python and R dependencies

Cell-type annotation

  • Cell-type annotation

Advanced plots

  • Advanced plots
    • Gene list format
    • Stacked violin plot
    • Multi-gene dot plot
Asc-Seurat: Analytical single-cell Seurat-based web application
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© Copyright Asc-Seurat, 2021. Pereira WJ, Almeida FM, Balmant KM, Rodriguez DC, Triozzi PM, Schmidt HW, Dervinis C, Pappas Jr. GJ, Kirst M.

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