NeoImmuno.scRNAseq.lineage_identification.Rmd:
R markdown script file for single cell RNAseq subpopulation identification/annotation and visulization, including major lineages (Lymphoid, Myeloid, Epithelial) and their sublineages.
NeoImmuno.scRNAseq.subpopulation.comparison.Rmd:
R markdown script file for differential comparisons, including including gene expression, percentages of sublineages for each cell major lineage across clinical conditions, such as tumor vs normal, across different treatment arms, smoking status, clinical outcomes, etc.