Troubleshooting & FAQ¶
Q: I see "Invalid credentials" when trying to log in. : Double-check that you are entering the correct username and password provided by Liragen. Credentials are case-sensitive. If the problem persists, contact Liragen support to have your credentials verified or reset.
Q: My project shows "- Not ready" in the Project dropdown. : This means the RNA-Seq analysis pipeline is still processing your data. Depending on dataset size, this may take some time. Check back later — once processing is complete, the label will be removed and all visualization tabs will be available.
Q: The plots are taking a long time to load. : Large datasets may take a few seconds to render. Ensure you have a stable internet connection. If performance is consistently slow, try narrowing your data using the gene ID or gene description filters in the sidebar, which reduces the amount of data being plotted.
Q: The Heatmap by Gene shows a message about "showing top 500 by variance." : When your dataset contains a very large number of genes, the heatmap automatically limits display to the top 500 genes ranked by variance across samples. This is done for readability. Use the sidebar filters to narrow down to specific genes of interest if you want to see a particular subset.
Q: The Bar chart says "Select gene descriptions to filtered in the sidebar to see the bar chart." : The Bar tab requires you to first select one or more gene descriptions using the Filter by gene desc dropdown in the sidebar. Once you have made a selection, the chart will appear.
Q: How do I create a new analysis project? : Click the New Project button at the bottom of the sidebar, enter one or more NCBI BioProject accession IDs (comma-separated), provide a project name, and click Fetch. Follow the on-screen steps to annotate your samples and define contrasts, then click Done to submit the project for analysis.
Q: Can I export or download the plots? : Streamlit-based plots support interactive features like hover tooltips and zoom. For static exports, you can use your browser's screenshot functionality or right-click on the plot to save the image (if supported by the chart library). For underlying data, expand the data table below each plot and copy or select the data as needed.
Q: Can I share my customized view with a colleague? : Customizations (colors, filters, thresholds) are session-specific and are not saved between sessions or shareable via URL. Each user should log in with their own credentials and adjust settings as needed.
Q: The Venn tab says "Venn diagram requires at least 2 contrast files." : Your project needs at least 2 DESeq2 contrast files to generate a Venn diagram. Projects with a single contrast cannot use this feature.
Q: The PPI tab says the organism is not available in STRING. : STRING DB does not cover all organisms. For non-model organisms (e.g., sweet potato), try entering a close model organism (e.g., Arabidopsis thaliana). Alternatively, use the Co-expression tab, which works for any organism without an external database.
Q: What browsers are supported? : Liragen Insights works best in modern browsers: Google Chrome, Mozilla Firefox, Microsoft Edge, and Apple Safari. Ensure your browser is up to date for the best experience.