Extended Data Fig. 4: Supplementary analysis for cluster-free differential abundance testing using Milo.
From: Dissecting gene regulatory networks governing human cortical cell fate
a-c. UMAPs showing results for differential abundance testing using Milo at the sgRNA level under ARX(a), NR2E1(b) and ZNF219(c) KD. (left) UMAPs of downsampled NT and perturbed cells on D7, colored by condition. (right) Neighborhood graphs. Node size denotes cell numbers in each neighborhood; edge depicts the number of cells shared between neighborhoods; node color denotes log2FC (FDR = 0.1) when perturbed. d-g. UMAPs showing results at the gene level under ARX(d), NR2E1(e), POU2F1(h), and BHLHE22(g) KD after downsampling to 200–600 cells.
