bedapub/melanomacitresponse_scrnaseq_tilandpbmc_publication

This repository includes notebooks utilized to produce results for the publication "Myeloid-T cell interplay, cell state transitions and checkpoint inhibitor response in melanoma"

MelanomaCITResponse_scRNAseq_TILandPBMC_publication

This repository includes notebooks utilized to produce results for the publication "Myeloid-T cell interplay, cell state transitions and checkpoint inhibitor response in melanoma":

• Standard workflow (adapted from besca 2.4, based on scanpy)
• Cell annotation workflow (adapted from besca 2.4, based on scanpy, including exploratory analyses related to signature and marker gene expression
• Velocity analysis notebooks for CD8T cell, CD4 T cell and Monocyte-macrophages (based primarly on scvelo)
• Notebooks used to generate differential cell expression, differential cell abundance and the publication figures

The underlying count data can be retrieved from ArrayExpress, E-MTAB-13770

Additional intermediate data not included as supplementary material in the publication due to format restrictions are included in data/:

• Additional Table 1. Cell type frequencies, related to Figures 1-2.
• Additional Table 2. Ratios of cell-cell interactions, related to Figure 3.
• Additional Table 3. P-values of cell-cell interactions, related to Figure 3.
• Additional Table 4. Latent time estimations, related to Figure 6.