Multi Sample Comparison

Compare expression, abundance, and pathways between test and control samples.

Differential Abundance

Select groups to compare

To run differential analyses between test and control samples:

  1. select an integrated dataset
  2. click samples comparison
  3. Open, fill out, and close the edit sample groups table
  4. Then specify test and control groups to compare
Download Comparison

Download differential analyses

To download the results of differential analyses between test and control samples select a cluster for group comparison then click download:

Download Comparison

Pseudobulk differential expression

Pseudobulk expression profiles are used for differential expression analyses between test and control groups.

Differential abundance

A differential abundance analysis is included in the downloaded results for any cluster. A grid-based differential abundance plot also allows you to visualize regions of differential abundance:

Differential Abundance

Pathway analyses

Dseqr runs Gene Ontology over-representation analysis of significantly up- and down-regulated genes. This uses a cached adaptation of goana.

Visual exploration

With samples comparison, select a gene to see expression side-by-side in test and control cells:

Compare Groups Plot

You are also shown the distribution of logcounts across each sample for the selected cluster:

Compare Samples Plot

You can also toggle the pseudobulk plot button to visualize regions of differential expression for the selected gene:

Compare Groups Pseudobulk Plot

Compare all clusters

To view genes that are consistently differentially expressed across clusters select All Clusters:

Compare All Clusters

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