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diff --git a/brain.documentation/QUICKSTART.rst b/brain.documentation/QUICKSTART.rst index 33a4a36..8a862df 100644 --- a/brain.documentation/QUICKSTART.rst +++ b/brain.documentation/QUICKSTART.rst @@ -1000,6 +1000,10 @@ As a utility, we can draw a scatterplot for an arbitrary pair of genes. This co At2g25930 At5g61380 sc +- Another way to view gene expression scatterplots is to use the **hypogen** program. Go to folder brain/code_review_drawScatterplot/hypogen, and type command ``python3 -m http.server`` to start the web app. Visit http://127.0.0.1:8000/scatterplot.html. + Enter two genes in the input fields "TF gene" and "Target gene", then click the Show button. + + .. note:: **Update gene expression levels** Hypogen stores gene expression levels across various conditions for each gene in JSON format (see the folder hypogen/json/). To update these JSON files, run Bash script ``update_gene_expression_json.sh``. Drawing sub-networks |