Commits · 2673f2f86d59165e1fb0f4c31e3bd7d9a74b51e0 · Strand Lab / sc-TissueMapper_Pr · GitLab

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Jun 18, 2018
- Add bash scripts for runnting TissueMapper and fix r.scripts to allow the... · 2673f2f8
  Gervaise Henry authored 6 years ago
```
Add bash scripts for runnting TissueMapper and fix r.scripts to allow the pipeline to run from bash script folder
```
  2673f2f8
- Fix VlnPlot for CCA · a5051b9d
  Gervaise Henry authored 6 years ago
  
  a5051b9d
- Change poststress res to 0.2 and copy parameters to DPrF · 6352d690
  Gervaise Henry authored 6 years ago
  
  6352d690
Jun 17, 2018
- Update DEGs from stable D17 analysis · 81564f59
  Gervaise Henry authored 6 years ago
  
  81564f59
- Reset parameters for D17 to work · 737034f2
  Gervaise Henry authored 6 years ago
  
  737034f2
Jun 16, 2018
- Revert "Tweak settings including incressing stress bin to 100, and use res 0.5 for St" · 70083761
  Gervaise Henry authored 6 years ago
```
This reverts commit 15294bb9.
```
  70083761
- Change post stress PC cutoff to 80% · 792f5605
  Gervaise Henry authored 6 years ago
  
  792f5605
- Tweak settings including incressing stress bin to 100, and use res 0.5 for St · 15294bb9
  Gervaise Henry authored 6 years ago
  
  15294bb9
Jun 15, 2018
- Fix D27 and D · 58946a86
  Gervaise Henry authored 6 years ago
  
  58946a86
- Update D · eb9a35b0
  Gervaise Henry authored 6 years ago
  
  eb9a35b0
- Update D17 · 79720d69
  Gervaise Henry authored 6 years ago
  
  79720d69
- Update D27 analysis · 9fbf24f7
  Gervaise Henry authored 6 years ago
  
  9fbf24f7
- Stop recalculation of hvg and PCA in subcluster, use PCs previously calcualted from combined data · 0a682c41
  Gervaise Henry authored 6 years ago
  
  0a682c41
- Fix OE dws deg file locations in DPrF analysis · e5e6248b
  Gervaise Henry authored 6 years ago
  
  e5e6248b
- Update D27 and DPr analysis · 10a236ec
  Gervaise Henry authored 6 years ago
  
  10a236ec
- Separate CCA1 and CCA2 violin plots to 2 separate plots · 4fcb1849
  Gervaise Henry authored 6 years ago
  
  4fcb1849
- Tweak D17 analysis · f4709c95
  Gervaise Henry authored 6 years ago
  
  f4709c95
- Change QuSAGE ID labeling to highest positive enrichment score, reguardless of FDR · 08b99e90
  Gervaise Henry authored 6 years ago
  
  08b99e90
Jun 14, 2018
- Add/update for DPrF (combine D17+D27, incuding CCA merge and phase) · 9ab54fb7
  Gervaise Henry authored 6 years ago
  
  9ab54fb7
- Fix project name for D27 · b23f21af
  Gervaise Henry authored 6 years ago
  
  b23f21af
- Fix stress genes to dws for D27 · ddaba369
  Gervaise Henry authored 6 years ago
  
  ddaba369
- Update D27 run code with current settings · 2f30f839
  Gervaise Henry authored 6 years ago
  
  2f30f839
- Revert hvg cutoffs in function based pipleine to fix cluster problems · 67aaa246
  Gervaise Henry authored 6 years ago
  
  67aaa246
- Revert stress binning to 50, and D17 settings · 01651421
  Gervaise Henry authored 6 years ago
  
  01651421
Jun 13, 2018
- Update function based D17 analysis · eb705ded
  Gervaise Henry authored 6 years ago
  
  eb705ded
- Make sress ID less conservative (50 bins to 100) · fff8053c
  Gervaise Henry authored 6 years ago
  
  fff8053c
Jun 12, 2018
- Reduce PC's calculated to 25 · 71be9687
  Gervaise Henry authored 6 years ago
  
  71be9687
Jun 11, 2018
- Change hvg cutoffs · 2104fb92
  Gervaise Henry authored 6 years ago
  
  2104fb92
- Fix Lin QuSAGE and rm commands · 9f68003a
  Gervaise Henry authored 6 years ago
  
  9f68003a
Jun 10, 2018
- Add code for D27 run with dws.sc genesets to function based pipeline · b02878f8
  Gervaise Henry authored 6 years ago
  
  b02878f8
- Fix finction based pipeline to use dws.sc DEGs · 1220c547
  Gervaise Henry authored 6 years ago
  
  1220c547
- Changer Stress DEG to be 5FC in script and replace geneset · ae0cf3b1
  Gervaise Henry authored 6 years ago
  
  ae0cf3b1
- Add DEGS genereated by function based pipeline · b3a6e22a
  Gervaise Henry authored 6 years ago
  
  b3a6e22a
- Update code for function based pipeline · 730cd621
  Gervaise Henry authored 6 years ago
  
  730cd621
Jun 09, 2018
- Add commands to save data to function based pipeline · 3dda395a
  Gervaise Henry authored 6 years ago
  
  3dda395a
- Update function based pipeline · 6f78ff2d
  Gervaise Henry authored 6 years ago
  
  6f78ff2d
Jun 05, 2018
- Make function based pipeline · 543fc2f0
  Gervaise Henry authored 6 years ago
  
  543fc2f0
Jun 01, 2018
- update DEG Stress and NE genesets · f1b1b031
  Gervaise Henry authored 6 years ago
  
  f1b1b031
May 31, 2018
- Fix gene nane errors in external NE genelist · 7b136f8d
  Gervaise Henry authored 6 years ago
  
  7b136f8d
- Add DIY script for CCA aggregation of D17 and D27 and increase resolution of downstream analysis · a03c163c
  Gervaise Henry authored 6 years ago
  
  a03c163c