Commits · a03c163c4c6e815a6ff3ca4ec1fa20efe38ae046 · Strand Lab / sc-TissueMapper_Pr · GitLab

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May 31, 2018
- Add DIY script for CCA aggregation of D17 and D27 and increase resolution of downstream analysis · a03c163c
  Gervaise Henry authored 6 years ago
  
  a03c163c
May 23, 2018
- Fix MergeSubClusts to handle Lineage ? pops as St · c6d84916
  Gervaise Henry authored 6 years ago
  
  c6d84916
May 22, 2018
- Update DIY.D17, make png's for heatmaps, make greyscale CustCol for global... · 8911edab
  Gervaise Henry authored 6 years ago
```
Update DIY.D17, make png's for heatmaps, make greyscale CustCol for global res0.1, make blue/red CustCol for global Lineage
```
  8911edab
- Update DWS sc DEGs · bb7d9692
  Gervaise Henry authored 6 years ago
  
  bb7d9692
- Change St cell type DEGs to generate compared to St · 5989f0d2
  Gervaise Henry authored 6 years ago
  
  5989f0d2
- Stop plotting stress hist · b82076e6
  Gervaise Henry authored 6 years ago
  
  b82076e6
- Add DIY visualizations for D27 (merge duplicated pops, re-make merge.ID, SubClust, Highlights) · 24243f74
  Gervaise Henry authored 6 years ago
  
  24243f74
- Add DIY visualizations for D17 (merge duplicated pops, re-make merge.ID,... · a68dc49e
  Gervaise Henry authored 6 years ago
```
Add DIY visualizations for D17 (merge duplicated pops, re-make merge.ID, SubClust, Highlights, LinSubClust Heatmaps)
```
  a68dc49e
May 20, 2018
- Make one set of tables with all samples · df3be2f8
  Gervaise Henry authored 6 years ago
  
  df3be2f8
- Add D27 bash script · b8336818
  Gervaise Henry authored 6 years ago
  
  b8336818
- When use DWS NE geneset, use 100 bins (instead of 50) for NE-Score (PC1) turning point choice · cbe5d3fa
  Gervaise Henry authored 6 years ago
  
  cbe5d3fa
May 19, 2018
- Update DWS sc genesets · 6f0425a9
  Gervaise Henry authored 6 years ago
  
  6f0425a9
- Tweak var.genes/PC/resolution selection · 7c97ee65
  Gervaise Henry authored 6 years ago
  
  7c97ee65
May 16, 2018
- Add Rplot.pdf to .gitignore · 88619b53
  Gervaise Henry authored 6 years ago
  
  88619b53
- Tweak cutoffs for var.genes · f27f7a31
  Gervaise Henry authored 6 years ago
  
  f27f7a31
- Add custom var.gene and %mito cutoffs and PC choices · 81f06892
  Gervaise Henry authored 6 years ago
  
  81f06892
May 14, 2018
- Change find cutoff in PCA for Stress and NE to first local minima after global maxima · 6a0e0cb8
  Gervaise Henry authored 6 years ago
  
  6a0e0cb8
- Fix sc labels for St QuSAGE · 72c642e8
  Gervaise Henry authored 6 years ago
  
  72c642e8
May 13, 2018
- Fix Stress PCA · 80cfe5b5
  Gervaise Henry authored 6 years ago
  
  80cfe5b5
- Fix minor Stress PCA error · 1b84d533
  Gervaise Henry authored 6 years ago
  
  1b84d533
- Change Stress cell determination back to PC1 · 945d7e94
  Gervaise Henry authored 6 years ago
  
  945d7e94
- Merge branch 'master' of git.biohpc.swmed.edu:StrandLab/sc-TissueMapper_Pr · c9dc1124
  Gervaise Henry authored 6 years ago
  
  c9dc1124
- Update D17 bash script · 96eee387
  Gervaise Henry authored 6 years ago
  
  96eee387
- Update DWS sc genesets · 595c7c82
  Gervaise Henry authored 6 years ago
  
  595c7c82
- Convert PC analysis to use KDE instead of K-means · ccc2f2ef
  Gervaise Henry authored 6 years ago
  
  ccc2f2ef
- Change PC's to be top 80% of 25 calculated · b1cd9556
  Gervaise Henry authored 6 years ago
  
  b1cd9556
May 10, 2018
- Update README.md · f4d7c67d
  Gervaise Henry authored 7 years ago
  
  f4d7c67d
- Update README.md *Add ORCID for GHH and DWS · ecce4746
  Gervaise Henry authored 7 years ago
  
  ecce4746
May 09, 2018
- Fix sc_QuSAGE_StSubClust.R for scDEG · 2ed11adf
  Gervaise Henry authored 7 years ago
  
  2ed11adf
- Fix rm(UK) in sc_QuSAGE_StSubClust.R · a438832c
  Gervaise Henry authored 7 years ago
  
  a438832c
- Update bash script FullAnalysis for D17PrF to do higher res analysis · 7b811154
  Gervaise Henry authored 7 years ago
  
  7b811154
- Update genesets with new scDEGs, including new Leu set · 6af28f5f
  Gervaise Henry authored 7 years ago
  
  6af28f5f
- Fix sc_DEG.R to work with identified Leukocyte clusters, also fix other r.scripts to handle them · 33aa56f1
  Gervaise Henry authored 7 years ago
  
  33aa56f1
May 07, 2018
- Update QuSAGE codes to correlate to DWS sc Pop DEGs · c9536e9e
  Gervaise Henry authored 7 years ago
  
  c9536e9e
- Add GO Leukocyte Activation geneset · e4a117e1
  Gervaise Henry authored 7 years ago
  
  e4a117e1
May 03, 2018
- Fix MergeSubClust problem with repeated idents, in particular Endo vs EndoC · c2a5d641
  Gervaise Henry authored 7 years ago
  
  c2a5d641
- Add calculated Epi and St DEGs to geneset from D17PrF · cc1c850e
  Gervaise Henry authored 7 years ago
  
  cc1c850e
- Make pan-Epi and pan-St DEG lists · 27799312
  Gervaise Henry authored 7 years ago
  
  27799312
May 01, 2018
- Add D17PrF DEGs for each population, updating scNE and scStress · 1db9f6a9
  Gervaise Henry authored 7 years ago
  
  1db9f6a9
- Fix sc_DEG.R · e94edb7c
  Gervaise Henry authored 7 years ago
  
  e94edb7c