Merge Single Cell Counts

This tool combines multiple matrices into a single count matrix for downstream analysis. The Merge Single Cell Counts function does not conduct Data Integration; rather, it consolidates multiple count tables into a unified dataset. This enables the specification of an experimental design, facilitating subsequent integration as an intermediate step in the clustering process. Additionally, it provides the capability to visualize violin plots of multiple samples within a single plot, as illustrated in Figure 1.

This feature is designed to enhance the ease of specifying experimental designs, and in consideration of the unique characteristics of library construction in droplet-based technologies such as 10x Chromium or Drop-seq. In these technologies, Cell Barcodes may be duplicated across samples, resulting in different cells being identified with the same Cell Barcodes. To address this, the Merge Single Cell Counts function appends a distinct suffix to all cells within a given count table, ensuring uniqueness across samples.

Input

This tool only accepts OmicsBox scRNA-Seq Count Matrices in .box format. They can be obtained with the scRNA-Seq Quantification tool or loaded into OmicsBox from external files.

• Merge Single Cell Counts: Combine count matrices into a single count matrix for downstream analysis such as clustering and trajectory analysis. On the opened wizard, select the count matrices in .box format to merge with the opened one (Figure 13). Cell barcodes will be unique for each sample (sequencing library) but features will be merged together whenever they match. See warning panel below .
• Experimental Design: Assign factors (e.g. disease, age, sex, etc.) and assign a condition to each sample (count matrix). This makes sense after having merged count matrices together and can simplify the configuration of downstream analysis. On the opened wizard (Figure 14), press "Add Factor" to add a column and type the conditions on the given cells. Alternatively, press "Load Design" to specify the experimental design in a text file. Once specified, click on "Run".

Figure 1. Violin plot showing multiple samples.

Run Merge Single-cell Counts

Go to transcriptomics → Single Cell RNA-Seq → Merge Single Cell Counts.

Input

Select all the count tables to merge by clicking on the "Add Files" button (Figure 2).

Configuration

Specify the experimental factors (if any) (Figure 3). In order to add a factor, click on the "Add Factor" button. Then, write the factor name on the box and the conditions in the new column, next to each sample. Do not press enter, click anywhere on the wizard once finished writing.

Once finished, click on "Run". The experimental factors will be stored as cell metadata.

Figure 2. Input wizard page.

Figure 3. Specify the experimental factors for each count table.