Clusters app

Please note that this app is best viewed on a desktop or with landscape mode on a tablet computer. Some visualizations are large in width and may display unexpected behaviour on mobile devices.

1 Input sidebar

1.1 Gene input

Users may choose to type desired gene names into the text box, or upload a list of genes. Please use the toggle button below the gene input textbox to activate the file upload mode.

1.1.1 Text box gene entry

Please note that while typing gene names into the text box, suggestions will appear in a drop-down menu below the text that you type. Suggested genes are from the gene annotation of this atlas, i.e. the genes that were investigated using single-cell RNA seq. However, some of these genes had no detected expression in the brain regions contained in the atlas, so there was no data collected on them. If you choose to query a gene that is in the annotation but not in the dataset, you will receive an error message.

1.1.2 Gene list file type and formatting

Users may upload gene lists in .txt, .csv, or .tsv format.

All .txt files provided to the app must have one gene on each line of the file. For .csv files and .tsv files, we recommend using the default separation (i.e. comma-separation or tab-separation respectively) between genes.

1.1.3 Gene input validation

The app will display an error message if gene(s) provided as input do not match with any of the genes in the atlas. An error message with the unrecognized gene name should be displayed in this case instead of the relevant plots. In some cases, genes were present in the annotation of the atlas, but no data was collected on them. (See the Text box gene entry section above for more information.) In this case, you will receive a descriptive error describing this situation.

Note: In the case of the timecourse tab, error messages are only displayed when selecting the unrecognized gene for display, since only one gene's plot can be shown at a time. In the case of the clusters ranked by expression tab, if the option for mean gene expression is off, only the first gene's plot is displayed, and therefore an error will only occur if the first gene is unrecognized.

1.1.4 Troubleshooting gene list upload

Please check the following specifications if you are having trouble uploading a gene list to the app:

• Please check the capitalization of your gene names. The app's input is case-sensitive and will only accept matching capitalizations. The required capitalization convention (common for mouse gene names) is to capitalize only the first letter of the gene name (e.g. "Pdgfra", not "PDGFRA")
• Please check your file for whitespace. If you have included extra empty lines in your file, this may cause errors. Additionally, gene names containing whitespace (e.g. "Neurod2 " or " Dlx1") will not be accepted by the app as it is whitespace-sensitive.
• The app is built to read files encoded in UTF-8 format. If your file encoding is different (e.g. Latin1) the app may behave unexpectedly.

1.2 Bookmarking

The braindex clusters app currently implements a URL bookmarking system, where the current state of the app is stored as variables within a URL. You can bookmark this URL or otherwise save it to preserve the current settings of the app.

Important note: The URL bookmarking system only saves input genes from the textbox, and not the contents of uploaded gene lists. That is, if you saved the state of the app when it displayed genes from a gene list, you will need to upload the same file to the app once you have opened the URL.