Frequently asked questions

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Click "Datasets" on the main menu, then click "Samples", each row in the list represents one single cell sequencing sample. To explore any sample simply press "view".
Click "Datasets" on the main menu, then click "Samples", select "view" for the experiment of interest (for example this one). Type the gene symbol in the "Gene search" box and press "Show". The plot will be shown on the bottom of the page. Multiple genes can be separated with commas. Colors correspond to the clusters in the t-SNE/UMAP plots.
Click "Datasets" on the main menu, then click "Cell type markers", on the right side there is a link called flag, press it and send a report. New markers can be added to the list through this submission form.
Click "Datasets" on the main menu, then click "Cell type markers", there is a link "get csv file" on the top of the page.
Click "Datasets" on the main menu, then click "Samples", then select an experiment you are interested in and press view on the right side. On the bottom of the page that open there is a download link to a sparse matrix wrapped inside an R data file.
Click "Search" on the main menu, and in the search box type your genes separated by 'AND'. For example, a query like this one below will list cell clusters where *BOTH* CD4 and CD8a are expressed:
							CD4 and CD8a
							
When using a boolean search, expression levels and ranks are not shown.
Click "Search" on the main menu, and in the search box type:
							X not Y
							

Example where X and Z are required to be expressed and Y is not expressed:

							X and Z not Y
							
When using a boolean search, expression levels and ranks are not shown.
Click "Datasets" on the main menu, then click "Samples", then select an experiment you are interested in and press view on the right side. On the bottom of the page that open there is a download link called "Cell clustering results".
There is not a mechanism for that at the moment. It could be implemented at a later stage.
We scan NCBI's Sequence Read Archive for new studies on a regular basis and process data in a standardized pipeline. We don't store the original sequencing reads.
A manuscript is currently in preparation. In the meantime the database can be cited as:

Franzén O & Björkegren J. PanglaoDB - a database for exploration of single cell RNA sequencing data: https://panglaodb.se

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The name is a tribute to the island of Panglao.