Commits · 96eee38719fc1c07bf04cea1dc9495e8cec632ce · Strand Lab / sc-TissueMapper_Pr · GitLab

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May 13, 2018
- 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 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
- Turn off vector.friendly in TSNEPlot because of X11 errors · 384aa380
  Gervaise Henry authored 7 years ago
  
  384aa380
Apr 30, 2018
- Fix Epi QuSAGE · 570d5e70
  Gervaise Henry authored 7 years ago
  
  570d5e70
- Fix St QuSAGE · 8e373bac
  Gervaise Henry authored 7 years ago
  
  8e373bac
- Fix patition name for sc_FullAnalysis-D17PrF.sh · 58e8a049
  Gervaise Henry authored 7 years ago
  
  58e8a049
- Make QuSAGE for Lineage and Epi use DWS 5FC DEGs · 2d5d563b
  Gervaise Henry authored 7 years ago
  
  2d5d563b
- Add 0FC and 5FC DWS DEGs to genesets · e2445447
  Gervaise Henry authored 7 years ago
  
  e2445447
Apr 29, 2018
- Fix DWS DEG's again · 1bfa5d45
  Gervaise Henry authored 7 years ago
  
  1bfa5d45
- Fix DWS DEGs · 04f17171
  Gervaise Henry authored 7 years ago
  
  04f17171
- Add back Cell Cycle analysis to default FullAnalysis sh · e4e48987
  Gervaise Henry authored 7 years ago
  
  e4e48987
- Add FullAnalysis sh with all defaults · 0d104d4d
  Gervaise Henry authored 7 years ago
  
  0d104d4d
- Make default demultiplex file group number = 1 · f0fd7e61
  Gervaise Henry authored 7 years ago
  
  f0fd7e61
- Update FullAnalyis sh from Pr to D17PrF · 21f4f870
  Gervaise Henry authored 7 years ago
  
  21f4f870
- Add library readr to sc_DEG.R · 1caf21f6
  Gervaise Henry authored 7 years ago
  
  1caf21f6
- Update DWS DEGs · faca7854
  Gervaise Henry authored 7 years ago
  
  faca7854
Apr 27, 2018
- Have sc_Demultiplex us generic aggrigation_csv.csv file · 799956db
  Gervaise Henry authored 7 years ago
  
  799956db
Apr 25, 2018
- Downsample data for QuSaGE before converting to dataframe to handle large datasets · b76082ea
  Gervaise Henry authored 7 years ago
  
  b76082ea
Apr 20, 2018
- Load 'methods' package at the start of every R script as Rscript no longer auto loads it · 6b964918
  Gervaise Henry authored 7 years ago
  
  6b964918
- Upgrade to R/3.4.1 · 91f3a49e
  Gervaise Henry authored 7 years ago
  
  91f3a49e
Apr 19, 2018
- Add 128GB and 384GB partitions as option for FullAnalysis bash scripts, also... · 04269b42
  Gervaise Henry authored 7 years ago
```
Add 128GB and 384GB partitions as option for FullAnalysis bash scripts, also clean up all bash scripts
```
  04269b42
- Increase num.cores for parallel processing to 50 · d2298ee5
  Gervaise Henry authored 7 years ago
  
  d2298ee5
Apr 16, 2018
- Make points on scatter plots (tSNEPlot/DimPlot) png (not vector) with vector.friendly=TRUE · 7312d6f9
  Gervaise Henry authored 7 years ago
  
  7312d6f9
Apr 12, 2018
- Add multi-core parallel processing support to ScaleData Seurat function · 549aab94
  Gervaise Henry authored 7 years ago
  
  549aab94
- Fix sc_QuSAGE_Epi/SubSubClust.R tSNE output filenames · 516d149b
  Gervaise Henry authored 7 years ago
  
  516d149b
Apr 11, 2018
- Update .gitignore to ignore WR/ · 30d61dc4
  Gervaise Henry authored 7 years ago
  
  30d61dc4