Using a Custom Gene Set in Singscope

Overview

This vignette explains how to upload and analyse a custom gene set in the app.

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File Format

Upload a .csv or .tsv file with the following two columns:

Pathway	Gene
TEST123	PMEL
TEST123	MLANA
TEST123	SOX10

Column names must be exactly Pathway and Gene.

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Uploading

1. Navigate to the Import Data section.
2. Use the “Upload Custom Gene Set” input to upload your file.
3. Click Submit Data.

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Output

Once uploaded:

• The app will automatically parse your file and use it to compute singscores.
• You’ll see your gene set(s) under “Genes in Selected Signature(s)”.
• Merging with the default dataset is automatically disabled for custom gene sets.

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Example File

Here is a valid example saved as CSV:

Pathway,Gene
TEST123,PMEL
TEST123,MLANA
TEST123,SOX10