Single-cell Lung Cancer Atlas

The core atlas was compiled from 21 datasets comprising 505 samples from 298 patients. 38 different cell-types were annotated at different levels of granularity.

By using the transfer learning method scArches another 8 datasets were projected onto the core atlas, resulting in an extended atlas with 1.3 million cells, 556 samples and 318 patients.

CZI cell-x-gene portal

Both core and extended atlas are available on the CZI cell-x-gene. There, you can explore the datasets interactively in the browser and download them as h5ad (scverse) or rds (Seurat) files with standardized metadata for further analysis.

scArches model

For the core atlas, we also provide a scArches model that allows to project new datasets onto the atlas and automatically annotate cell-types.

Get input data and intermediate results

In addition to the h5ad objects mentioned above, we provide preprocessed input data, intermediate results and final results on zenodo. The results were derived using the source code provided on GitHub and contain a rendered version of the Jupyter/Rmarkdown notebooks that were used to generate the figures in the manuscript.

Browse code

All code needed to reproduce the study is wrapped into a nextflow workflow and publicy available from GitHub.

Contact

For reproducibility issues or any other requests regarding single-cell data analysis, please use the issue tracker. For anything else, you can reach out to the corresponding author(s) as indicated in the manuscript.