Put in a gene to see 2D/3D tSNE plots
P6 mouse tibia 10x cells (Figure 1E)
(genotype: C10Cre;Irx3+/ΔHCIrx5+/-; Rosa26LSL-tdTomato/+ Het)


Select a cell set:

2D or 3D? 2D 3D
with violin plot? no linear all log all linear pos-only log pos-only
tSNE or PCA? tSNE PCA UMAP SCT->CCA SCT->tSNE SCT->UMAP
Cell grouping? Lock to color codes

Point size? (2)
Point size for zero values? (3)




e.g. CD24, MGP, GREM1





Cutoff:



Only first valid pathway will be shown.
Cutoff:

The all-positive (or your specified) cells will be shown
(To specify a neg marker: add a neg sign before gene.)
-or-

Cutoff:
choose a dot-shape scheme:
Scaled or not scaled by num gene expressed per cell?
choose a color scheme for all-pos:



Multiple pathways are accepted. Union of pathway genes taken.
Over 500 genes could be slow.
Cutoff:  
How to evaluate pathway activity?  
Cutoff:









Last modified: Thursday, March 23, 2023 09:18:57
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