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:

• AI analysis methods summary
• AI analysis suggestions
• Task actions
• Data summary report
• QA/QC

  • Feature distribution
  • Imported count matrix report
  • Single-cell QA/QC
  • Cell barcode QA/QC
  • 5-base Methylation QC
• Annotation/Metadata

  • Annotate cells
  • Annotate features
  • Publish cell attributes to project
  • Attribute report
• Pre-analysis tools

  • Pseudobulk
  • Split by feature type
  • Generate group cell counts
  • Merge matrices
  • Generate beta value
  • Generate methylation mvalues
• Filtering

  • Filter features
  • Filter samples/cells
  • Split by attribute
  • Downsample cells
• Normalization and scaling

  • Normalization
  • Normalize to housekeeping genes
  • Normalize to baseline
  • Scran deconvolution
  • TF-IDF normalization
  • Impute missing values
  • Impute missing values
  • Impute low expression
  • SCTransform
• Batch removal

  • General linear model
  • Harmony
  • Seurat3 integration
• Statistics

  • Differential Analysis

    • DESeq2
    • Hurdle model
    • ANOVA/LIMMA-trend/LIMMA-voom
    • Welch's ANOVA
    • Kruskal-Wallis / Wilcoxon
    • Poisson/Negative binomial/GSA (Gene Specific Analysis)
    • Troubleshooting
  • Descriptive statistics
  • Correlation
  • QTL analysis
  • Differential methylation
  • Detect differential methylation
  • Compute biomarkers
  • Survival Analysis with Cox regression and Kaplan-Meier analysis
  • Classification
  • Spatially Variable Genes
• Exploratory analysis

  • Graph-based clustering
  • K-means clustering
  • Compare clusters
  • PCA
  • t-SNE
  • UMAP
  • Hierarchical clustering / heatmap
  • AUCell
  • Find multimodal neighbors
  • SVD
  • CellPhoneDB
  • BANKSY - Spatial Domain Identification
  • Merge differential expression results
• Region analysis

  • Get Regional Methylation
  • Annotate Regions
• Trajectory analysis

  • Trajectory Analysis (Monocle 2)
  • Trajectory Analysis (Monocle 3)
• Variant Analysis

  • Annotate Variants
  • Annotate Variants (SnpEff)
  • Annotate Variants (VEP)
  • Filter Variants
  • Summarize Cohort Mutations
  • Combine Variants
  • Filter variants with databases
  • Create genotype matrix
• Combine multiomics data

  • Combine 5-base methylation and variant data
• Motif Detection
• Biological interpretation

  • Gene set enrichment
  • GSEA
  • Gene set ANOVA
  • Correlation Engine atlases
  • Correlation Engine pathway
  • Get targeted mRNA
• Classification

  • Classify cell type
  • Train classifier
  • ScType
• Conversion
• Region analysis

  • Annotate regions