just adds a directory with my contribution under /hacks #7
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Foreman bulk RNA-seq dataset - genes from CD4 and CD8 granuloma cells with negative association with logCFU (TB protective). Confirmation of this relationship in different celltypes from the Bromley pseudobulk dataset.
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i looked at the Foreman granuloma dataset. I separately modeled expression by logCFU in both CD4 and CD8 cells. I plotted genes with FDR < 0.2 and a negative relationship to logCFU. Then I took that same genelist and pulled out the genes from the Bromley dataset. I plotted the top five clusters for each of the Foreman-derived genes with FDR < 0.2 in ANY cluster (independent of group). And I saw some relationship to group, so I also plotted the group-wise slopes within coarse cluster and the associated interaction FDR value.