Task Menu

The Task Menu lists all the tasks that can be performed on a specific node. It can be invoked from either a Data or Task node and appears on the right hand side of the Analyses tab. It is context-sensitive, meaning that it will only present tasks that the user can perform on the selected node. For example, selecting an Differential analysis report data node will not present normalization as options.

Clicking a Data node presents a variety of tasks:

• Task actions

• Data summary report

• QA/QC

  • Feature distribution

  • Single-cell QA/QC

  • Cell barcode QA/QC

• Annotation/Metadata

  • Annotate cells

  • Annote features

  • Publish cell attributes to project

• Pre-analysis tools

  • Pseudobulk

  • Split by feature type

  • Generate group cell counts

  • Merge matrices

• Filtering

  • Filter features

  • Filter samples or cells

  • Split by attribute

  • Downsample Cells

• Normalization and scaling

  • Normalization

  • Normalize to baseline

  • Scran deconvolution

  • SCTransform

  • TF-IDF normalization

  • Normalize to housekeeping genes

  • Impute low expression

  • Impute missing values

• Batch removal

  • General linear model

  • Harmony

  • Seurat3 integration

• Statistics

  • Differential Analysis

    • DESeq2

    • Hurdle model

    • ANOVA/LIMMA-trend/LIMMA-voom

    • Kruskal-Wallis

    • GSA (Gene Specific Analysis)

    • Troubleshooting

• Correlation

• Compute biomarkers

• Survival Analysis with Cox regression and Kaplan-Meier analysis - Partek Flow

• Exploratory Analysis

  • Graph-based Clustering

  • K-means Clustering

  • Compare Clusters

  • PCA

  • t-SNE

  • UMAP

  • Hierarchical Clustering

  • AUCell

  • Find multimodal neighbors

  • SVD

  • CellPhoneDB

• Trajectory Analysis

  • Trajectory Analysis (Monocle 2)

  • Trajectory Analysis (Monocle 3)

• Biological Interpretation

  • Gene Set Enrichment

  • GSEA

• Classification

  • Classify cell type

  • Train classifier

  • SCtyp

• Data Viewer

• Settings