search

HorvathLab / NGS

Next-Gen Sequencing tools from the Horvath Lab
https://horvathlab.github.io/NGS/
MIT License
39 stars 16 forks source link

MB figure requests #46

Open smartinezzz opened 2 months ago

smartinezzz commented 2 months ago

  1. Plot 2.2, 2.3, and 2.4 presenting HAND-specific up- and down-regulated pathways and genes for each cell population, including neurons.

  2. From PMID: 37774676. Please make the following figures : Fig. 3A (genes should be from inflammation/trained immunity, glycolysis and cholesterol pathways), Fig. 6F (again, the same genes and pathways).

  3. From PMID:36593328. Please recreate Fig. 2 with our genes and pathways.

  4. From PMID: 36447241. Please make Fig. 2B using our cell types as clusters.

  5. From PMID: 38867657. Please make Fig. 1, Fig. 5D, Fig. 5G, and Fig. 5H.

smartinezzz commented 1 month ago

Plot 2.2, 2.3, and 2.4 presenting HAND-specific up- and down-regulated pathways and genes for each cell population, including neurons.

This is complete and these are located here: /data/lab/smart/projects/mb_snataq/figures

smartinezzz commented 1 month ago

PMID: 37774676 Figure 3A replicated; results here: /data/lab/smart/projects/mb_snataq/atac/figures. I did not make these with genes from inflammation, glycolysis and cholesterol pathways - I may need to redo that.

smartinezzz commented 1 week ago

Made dot plots for glia and neurons separately (with inflammation, glycol and cholmet as subplots) for genes and pathways

Made volcano plots for genes and pathways for each cluster

smartinezzz commented 1 week ago

From PMID: 37774676 6F for genes only (inflammation/trained immunity, glycolysis and cholesterol pathways) - I don't think there is a good way to do this for pathways

smartinezzz commented 3 days ago

PMID: 38867657 Fig. 5D - Anelia has said previously this is outside the scope of the project

Fig. 5G, and Fig. 5H should be covered by the other figures