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charliemcnulty

Charlie

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Vorinostat in PTL (840 donor)
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Tunicamycin in PTL (840 donor)
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ThiametG in PTL (840 donor)
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Taxol in PTL (840 donor)
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Rosiglitazone in PTL (840 donor)
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Rapamycin in PTL (840 donor)
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LiCl in PTL (840 donor)
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Compound81 in PTL (840 donor)
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Bardoxolone in PTL (840 donor)
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A971432 in PTL (840 donor)
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A366 in PTL (840 donor)
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17AAG in PTL (840 donor)
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Vorinostat in POD (840 donor)
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Tunicamycin in POD (840 donor)
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ThiametG in POD (840 donor)
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Taxol in POD (840 donor)
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Rosiglitazone in POD (840 donor)
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Rapamycin in POD (840 donor)
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LiCl in POD (840 donor)
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Compound81 in POD (840 donor)
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Bardoxolone in POD (840 donor)
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A971432 in POD (840 donor)
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A366 in POD (840 donor)
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17AAG in POD (840 donor)
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Tunicamycin in IPS (840 donor)
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ThiametG in IPS (840 donor)
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Taxol in IPS (840 donor)
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Rosiglitazone in IPS (840 donor)
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Rapamycin in IPS (840 donor)
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LiCl in IPS (840 donor)
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Compound81 in IPS (840 donor)
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Bardoxolone in IPS (840 donor)
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A971432 in IPS (840 donor)
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A366 in IPS (840 donor)
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17AAG in IPS (840 donor)
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Vorinostat in IPS (840 donor)
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Tunicamycin in IPS (840 donor)
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ThiametG in IPS (840 donor)
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Taxol in IPS (840 donor)
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Rapamycin in IPS (840 donor)
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Rapamycin in IPS (840 donor)
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LiCl in IPS (840 donor)
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Compound81 in IPS (840 donor)
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Bardoxolone in IPS (840 donor)
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A971432 in IPS (840 donor)
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A366 in IPS (840 donor)
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17AAG in IPS (840 donor)
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Vorinostat in PTL (AD3 donor)
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Tunicamycin in PTL (AD3 donor)
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ThiametG in PTL (AD3 donor)
Plot
Taxol in PTL (AD3 donor)
Plot
Rosiglitazone in PTL (AD3 donor)
Plot
Rapamycin in PTL (AD3 donor)
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LiCl in PTL (AD3 donor)
Plot
Compound81 in PTL (AD3 donor)
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A971432 in PTL (AD3 donor)
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A971432 in PTL (AD3 donor)
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A366 in PTL (AD3 donor)
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17AAG in PTL (AD3 donor)
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Vorinostat in POD (AD3 donor)
Plot
Tunicamycin in POD (AD3 donor)
Plot
Taxol in POD (AD3 donor)
Plot
Taxol in POD (AD3 donor)
Plot
Rosiglitazone in POD (AD3 donor)
Plot
Rapamycin in POD (AD3 donor)
Plot
LiCl in POD (AD3 donor)
Plot
Compound81 in POD (AD3 donor)
Plot
Bardoxolone in POD (AD3 donor)
Plot
A971432 in POD (AD3 donor)
Plot
A366 in POD (AD3 donor)
Plot
17AAG in POD (AD3 donor)
Plot
Vorinostat in IPS (AD3 donor)
Plot
Tunicamycin in IPS (AD3 donor)
Plot
ThiametG in IPS (AD3 donor)
Plot
Taxol in IPS (AD3 donor)
Plot
Rosiglitazone in IPS (AD3 donor)
Plot
Rapamycin in IPS (AD3 donor)
Plot
LiCl in IPS (AD3 donor)
Plot
Compound81 in IPS (AD3 donor)
Plot
Bardoxolone in IPS (AD3 donor)
Plot
A971432 in IPS (AD3 donor)
Plot
A366 in IPS (AD3 donor)
Plot
17AAG in IPS (AD3 donor)
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Vorinostat in PTL (AD2 donor)
Plot
Tunicamycin in PTL (AD2 donor)
Plot
ThiametG in PTL (AD2 donor)
Plot
Taxol in PTL (AD2 donor)
Plot
Rosiglitazone in PTL (AD2 donor)
Plot
Rapamycin in PTL (AD2 donor)
Plot
LiCl in PTL (AD2 donor)
Plot
Compound81 in PTL (AD2 donor)
Plot
Bardoxolone in PTL (AD2 donor)
Plot
A971432 in PTL (AD2 donor)
Plot
17AAG in PTL (AD2 donor)
Plot
17AAG in PTL (AD2 donor)
Plot
Vorinostat in POD (AD2 donor)
Plot
Tunicamycin in POD (AD2 donor)
Plot
Tunicamycin in POD (AD2 donor)
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ThiametG in POD (AD2 donor)
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Taxol in POD (AD2 donor)(new)
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Rosiglitazone in POD (AD2 donor) (new)
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Rapamycin in POD (AD2 donor) (new)
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LiCl in POD (AD2 donor) (new)
Plot
Compound81 in POD (AD2 donor) (new)
Plot
Bardoxolone in POD (AD2 donor) (new)
Plot
A971432 in POD (AD2 donor) (new)
Plot
17AAG in POD (AD2 donor) (new)
Plot
Rosiglitazone in POD (AD2 donor)
Plot
Rapamycin in POD (AD2 donor)
Plot
LiCl in POD (AD2 donor)
Plot
Compound81 in POD (AD2 donor)
Plot
Bardoxolone in POD (AD2 donor)
Plot
A971432 in POD (AD2 donor)
Plot
A366 in POD (AD2 donor)
Plot
17AAG in POD (AD2 donor)
Plot
Vorinostat in IPS (AD2 donor)
Plot
Tunicamycin in IPS (AD2 donor)
Plot
Tunicamycin in IPS (AD2 donor)
Plot
ThiametG in IPS (AD2 donor)
Plot
Taxol in IPS (AD2 donor)
Plot
Rosiglitazone in IPS (AD2 donor)
Plot
Rapamycin in IPS (AD2 donor)
Plot
LiCl in IPS (AD2 donor)
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Compound81 in IPS (AD2 donor)
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Bardoxolone in IPS (AD2 donor)
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A971432_IPS_AD2
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A336_IPS_AD2
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17AAG - IPS - AD2
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degs in ptl cells - 840 donor
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degs in pod in 840 donors
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degs in ips - 840 donor
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degs in ptl - ad3 donor
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degs in pod - ad3
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ips-ad3 donors
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in PTL - ad2 donors
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degs in pods in ad2 donor
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degs in ips - ad2
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ips
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pod
Plot
Plot
Rosiglitazone
Plot
Volcano Plot Rapamycin in AD3 Cells
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Volcano Plot Bardoxolone in 840 Cells
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new PODXL
Plot
New CYP24A1
Plot
new NANOG
Plot
Expression of PODXL in Cell Lines - nicer colours
Plot
phenotype all
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new 840 bar plot
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new AD3 bar plot
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new AD2 bar plot
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new IPS barplot
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new POD barplot
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new PTL barplot
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no. of degs of compounds in phenotype
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Volcano Plot Vorinostat in 840 Cells
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Volcano Plot Tunicamycin in 840 Cells
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Volcano Plot ThiametG in 840 Cells
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Volcano Plot Taxol in 840 Cells
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Volcano Plot Rosiglitazone in 840 Cells
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Volcano Plot Rapamycin in 840 Cells
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Volcano Plot LiCl in 840 Cells
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Volcano Plot Compound81 in 840 Cells
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Volcano Plot A971432 in 840 Cells
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Volcano Plot A366 in 840 Cells
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Volcano Plot 17AAG in 840 Cells
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Number of DEGs by Compound in 840 Cells
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Volcano Plot Vorinostat in AD3 Cells
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Volcano Plot Tunicamycin in AD3 Cells
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Volcano Plot ThiametG in AD3 Cells
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Volcano Plot Taxol in AD3 Cells
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Volcano Plot Rosiglitazone in AD3 Cells
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Volcano Plot LiCl in AD3 Cell
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Volcano Plot Compound81 in AD3 Cells
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Volcano Plot Bardoxolone in AD3 Cells
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Volcano Plot A971432 in AD3 Cells
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Volcano Plot A366 in AD3 Cells
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Volcano Plot A366 in AD3 Cells
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Volcano Plot 17AAG in AD3 Cells
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Number of DEGs by Compound in AD3 Cells
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Volcano Plot Vorinostat in AD2 Cells
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Volcano Plot Tunicamycin in AD2 Cells
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Volcano Plot ThiametG in AD2 Cells
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Volcano Plot Taxol in AD2 Cells
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Volcano Plot Rosiglitazone in AD2 Cells
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Volcano Plot Rapamycin in AD2 Cell
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Volcano Plot LiCl in AD2 Cells
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Volcano Plot Compound81 in AD2 Cells
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Volcano Plot Bardoxolone in AD2 Cells
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Volcano Plot Bardoxolone in AD2 Cells
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Volcano Plot A971432 in AD2 Cells
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Volcano Plot A971432 in AD2 Cells
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Volcano Plot A366 in AD2 Cells
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Volcano Plot 17AAG in AD2 Cells
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Number of DEGs by Compound in AD2 Cells
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Volcano Plot Vorinostat in PTL Cells
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Volcano Plot Tunicamycin in PTL Cells
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Volcano Plot ThiametG in PTL Cells
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Volcano Plot Taxol in PTL Cell
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Volcano Plot Rosiglitazone in PTL Cells
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Volcano Plot Rapamycin in PTL Cells
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Volcano Plot LiCl in PTL Cells
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Volcano Plot Compound81 in PTL Cells
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Volcano Plot Bardoxolone in PTL Cells
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Volcano Plot A971432 in PTL Cells
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Volcano Plot A366 in PTL Cells
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Volcano Plot 17AAG in PTL Cells
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Volcano Plot Vorinostat in POD Cells
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Volcano Plot Tunicamycin in POD Cells
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Volcano Plot ThiametG in POD Cell
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Volcano Plot Taxol in POD Cells
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Volcano Plot Rosiglitazone in POD Cells
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Volcano Plot Rapamycin in POD Cells
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Volcano Plot LiCl in POD Cells
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Volcano Plot Bardoxolone in POD Cells
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Volcano Plot Bardoxolone in POD Cells
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Volcano Plot A366 in POD Cells
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Volcano Plot A366 in POD Cells
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Volcano Plot A366 in POD Cells
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Volcano Plot 17AAG in POD Cells
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Number of degs per compound in POD
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Volcano Plot Vorinostat in IPS Cells
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Volcano Plot Tunicamycin in IPS Cells
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Volcano Plot ThiametG in IPS Cells
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Volcano Plot Taxol in IPS Cells
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Volcano Plot Rosiglitazone in IPS Cells
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Volcano Plot Rapamycin in IPS Cells
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Volcano Plot Rapamycin in IPS Cells
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Volcano Plot LiCl in IPS Cells
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Volcano Plot Compound81 in IPS Cells
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Volcano Plot Bardoxolone in IPS Cells
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Volcano Plot A971432 in IPS Cells
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Volcano Plot A366 in IPS Cells
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volcano plot 17AAG IPS
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Number of DEGs by Compound in IPS Cells
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plotBCV(dge)
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log2
Plot
Histogram of filtered counts and log-transformed
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histogram of counts to show distribution (removed outliers)
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ggplot(norm_counts_DMSO) + + geom_histogram(aes(x = IPS_840), stat = "bin", bins = 200) + + xlab("Raw expression counts") + + ylab("Number of genes")
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sample 1 distribution
Plot
Rapamycin
Plot
GSEA - BP - Vorinostat
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GSEA - BP - Tunicamycin
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GSEA - BP - ThiametG
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GSEA - BP - Rosiglitazone
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GSEA - BP - Rosiglitazone
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GSEA - BP - LiCl
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GSEA - BP - Compound81
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GSEA - BP - Bardoxolone
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GSEA - BP - A971432
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GSEA - BP- A366
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GSEA- BP - 17AAG
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CYP24A1
Plot
CYP24A1
Plot
NANOG expression levels
Plot
PODXL
Plot
PODXL
Plot
Plot
Plot
Plot
Plot
Plot
LiCl
Plot
volcano plot compound81
Plot
extended axis
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extended axis
Plot
Plot
volcano plot a97143
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volcano plot a366
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17AAG volcano plot
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volcanos
Plot
MAplot of ddsDE.ALL
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heatmap clustering across samples
Plot
PCA of donors of all compounds
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PCA of all compounds but labelled cell lines
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PCA - stembancc - all compounds
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barplot of degs of all compounds
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Heatmap of tunicamycin expression samples
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Heatmap of Bardoxolone samples
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PCA plot - Tunicamycin expression data. before deseq
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PCA - bardoxolone expression data. before deseq
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stembancc - PCA dmso expression values
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heatmap, comp <- comp %>% dplyr::filter(padj < 0.05, abs(log2FoldChange) > 1.5) # changing this to fit names into heatmap. Z scores
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top var 250 genes, norm = F
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top 250 genes