These scripts are provided to aid those wishing to re-analyzed the data from the paper by Andrews et al. (2023). Many simply run generic single-cell analysis steps, while others are specific to liver data. If you use these scripts as a basis for your own analysis please cite our paper below.
Andrews, TS. Nakib, D. et al. (in press) Multi-omic profiling reveals the immunological landscape in the healthy and PSC human liver. Hepatology.
Raw data can be found on GEO :
Processed data can be found at cellxgene
Various web applications have been developed to allow you to interact with this data directly, rather than reanalyzing it. Please see the links below:
Healthy Map: https://macparlandlab.shinyapps.io/generalmap/ https://macparlandlab.shinyapps.io/macrophages/ https://macparlandlab.shinyapps.io/lymphocytes/ https://macparlandlab.shinyapps.io/endothelial/ https://macparlandlab.shinyapps.io/cholangiocytes/ https://macparlandlab.shinyapps.io/b_cells/ https://macparlandlab.shinyapps.io/stellate/
Spatial Healthy: https://macparlandlab.shinyapps.io/healthylivermapspatialgui/
Spatial PSC: https://macparlandlab.shinyapps.io/shinypsc_spatialappgui/