Magellan: COVID-19 Omics Explorer

Magellan is a web application for the display and analysis of next-generation sequencing data with a focus on COVID-19. The application runs on the de.NBI cloud infrastructure. We focus specifically on single-cell sequencing data, but other omics data, such as epigenetic data, will also be integrated. The goal is to provide easy and open access to the highly relevant data of COVID-19 patients for the community.

We are constantly working on improving this app. If you have any comments, suggestions or critics please send us a note at: mail


All sequencing data was produced at BIH/Charité and at locations of our cooperation partners. Integrated datasets are public available in open archives.

  • HBEC and lung cells: SARS ‐CoV‐2 receptor ACE 2 and TMPRSS 2 are primarily expressed in bronchial transient secretory cells. EMBO
  • COVID-19 patients: COVID-19 severity correlates with airway epithelium–immune cell interactions identified by single-cell analysis. Nature Biotechnology


  • 2020/06/16: Single-Cell-Map can visualize gene expression.
  • 2020/06/15: COVID-19 data is available for data analysis.
  • 2020/06/15: There is a major update of the user interface. Users of Single-Cell-Map are able to select subsets of cells to analyze cell-types and sample distribution.
  • 2020/06/11: Great news: first COVID-19 patients data integrated. The data is not public yet but it will be available next days.
  • 2020/04/05: HBEC and lunc cell data integrated.
  • 2020/04/01: Hello world!

de.NBI Cloud

Magellan is hosted at the de.NBI Cloud. The de.NBI cloud is a fully academic cloud funded by the BMBF (grant number(s): 031A537B, 031A533A, 031A538A, 031A533B, 031A535A, 031A537C, 031A534A, 031A532B), free of charge for academic users, which provides compute resources as well as storage capacity for large-scale scientific projects.


We use Matomo to track access to Magellan in order to improve usability of the website. Thereby, we do not store any personal data.



Single-cell map displays cells in UMAP coordinates. Cell color indicate either cell type or gene expression level. Attaching gene expression is optional. You can use your cursor to select a set of cells. Selection of cells shows cell counts and expression levels in sublcuster. Double-click on map to reset selection.


Dataset 1: includes cells from lung tissue (12 donors, 39,778 cells) and cells derived from subsegmental bronchial branches (4 donors, 17,521 cells).
Dataset 2: includes data from 14 COVID-19 patients with multiple sampling times and sampling locations as well as cells from 5 control donors. Cells were derived from nasopharyngeal or pooled nasopharyngeal/pharyngeal swabs (NS), bronchiolar protected specimen brushes (PS), and bronchoalveolar lavages (BL).

Gene expression

Attach a single gene to visualize its expression in selected cells.