Chromatin Accessibility and Expression Analysis from Matrix
The workflow Chromatin Accessibility and Expression Analysis from Matrix takes a pair of an Expression Matrix (
) / (
) and a Peak Count Matrix (
) as input to jointly analyze scRNA-Seq and scATAC-Seq data originating from the same sample or samples. The workflow performs quality control, normalization and cell type prediction on the expressions.
It then combines the expression and peak matrices to perform clustering and dimensionality reduction. It produces:
- a normalized Expression Matrix () / ();
- a Dimensionality Reduction Plot (
) associated with the automated clusters, predicted cell types and additional cell annotations;
- a Heat Map (
), a Dot Plot (
), and a Violin Plot (
) with the predicted cell types as cell groups;
- a Cell Abundance Heat Map () with the automated clusters and predicted cell types as cell groups;
The workflow can be found in the Template Workflows section here:
Single Cell Workflows (
) | From Imported Data (
) | Chromatin Accessibility and Expression Analysis from Matrix (
)
If you are connected to a CLC Server via your Workbench, you will be asked where you would like to run the analysis. We recommend that you run the analysis on a CLC Server when possible.
Choose either one or more Expression Matrix () / () and Peak Count Matrix () or Select files for import and select the formats that are compatible with the selected inputs.
Read more about import options in Importing data.
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