Commits · b76082eaf3c3ab7e7f1550d3b61582227880324b · Strand Lab / sc-TissueMapper_Pr · GitLab

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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
Apr 09, 2018
- Integrate surface and nuclear protein localization into DEG generation · 98a5383d
  Gervaise Henry authored 7 years ago
  
  98a5383d
- Prevent error if anchor gene does not exist in data, PC.Score.Stress/NE.R · dcf314bc
  Gervaise Henry authored 7 years ago
  
  dcf314bc
- Allow DEG and Table r.scripts to run without NE ID · 7bd79114
  Gervaise Henry authored 7 years ago
  
  7bd79114
- LineageSubClust res tSNEs put in global directory when NoStress analysis selected · f2d4c8cc
  Gervaise Henry authored 7 years ago
  
  f2d4c8cc
- Sllow Epi/St SubClust Merge to have different resolutions · 0fc3462b
  Gervaise Henry authored 7 years ago
  
  0fc3462b
- Bring Stress/NE on top of tSNE in sc_PC.Score.Stress/NE.R · b636f3ff
  Gervaise Henry authored 7 years ago
  
  b636f3ff
Apr 06, 2018
- Update README.md · 49cf7c27
  Gervaise Henry authored 7 years ago
  
  49cf7c27
- Fix sizes in enrichment plots · 044d9041
  Gervaise Henry authored 7 years ago
  
  044d9041
- Add Lineage UK cells to St for analysis · e1baf4eb
  Gervaise Henry authored 7 years ago
  
  e1baf4eb
Apr 05, 2018
- Fix c2 QuSAGE variable name (qs.result.st.c2...) · cf73641c
  Gervaise Henry authored 7 years ago
  
  cf73641c
Apr 04, 2018
- Fix sc_QuSAGE_UKSubClust.R spelling error · eef2df90
  Gervaise Henry authored 7 years ago
  
  eef2df90
- Fix tSNE file names for SubClust's · 819df513
  Gervaise Henry authored 7 years ago
  
  819df513
- Change c2 to c2.cp.kegg and c5 to c5.bp, include gmt's from MSigDB and change... · a0070df6
  Gervaise Henry authored 7 years ago
```
Change c2 to c2.cp.kegg and c5 to c5.bp, include gmt's from MSigDB and change reference in sc_QuSAGE_Epi/StSubClust.R
```
  a0070df6
Apr 03, 2018
- Run sc_FullAnalysis-Pr.sh on both 256GB and 256GBv1 partitions · 6b6fc6c9
  Gervaise Henry authored 7 years ago
  
  6b6fc6c9
Mar 30, 2018
- Add code to create and analize Continual Integreation test data · 112f3c32
  Gervaise Henry authored 7 years ago
  
  112f3c32
Mar 29, 2018
- Fix sc_PC.Score.NE.R's no downsampling... again · cf1fb9f8
  Gervaise Henry authored 7 years ago
  
  cf1fb9f8
- Fix Epi.sub name in sc_PC.Score.NE.R · 73c25a71
  Gervaise Henry authored 7 years ago
  
  73c25a71
- Fix sc_LineageSubClust.R to handle if UK Lineage cluster is present · 1c13edd1
  Gervaise Henry authored 7 years ago
  
  1c13edd1
- Generalize sc_LinkData.sh to handle any dataset by project (dir) name · 6a30b150
  Gervaise Henry authored 7 years ago
  
  6a30b150
Mar 28, 2018
- Add bash script to link 10x data to correct location (Pr data) · 2496a6ed
  Gervaise Henry authored 7 years ago
  
  2496a6ed
Mar 27, 2018
- Add no downsampling (NA) as an option for sc_PC.Score.NE.R · f2285a20
  Gervaise Henry authored 7 years ago
  
  f2285a20
- Add no downsampling (NA) as an option for sc_PC.Score.Stress.R · b303a7b0
  Gervaise Henry authored 7 years ago
  
  b303a7b0
Mar 26, 2018
- Add missing sc_MergeSubClust.R to bash.script · 874de560
  Gervaise Henry authored 7 years ago
  
  874de560
Mar 23, 2018
- Fix formatting in README.md (list indents · 0fc78b2b
  Gervaise Henry authored 7 years ago
  
  0fc78b2b
- Remove outdated (non-SubClust) QuSAGE .R files · b8fa588e
  Gervaise Henry authored 7 years ago
  
  b8fa588e
- Finalize SubClust analysis · 459fe2d0
  Gervaise Henry authored 7 years ago
  
  459fe2d0
Mar 19, 2018
- Add sc_MergeSubClust.R · 712d9bc6
  Gervaise Henry authored 7 years ago
  
  712d9bc6
- Fix input Rda file for sc_QuSAGE_StSubClust.R · 888f9c1a
  Gervaise Henry authored 7 years ago
  
  888f9c1a
Mar 18, 2018
- Add St QuSAGE for UK clusters · 03cc2e3f
  Gervaise Henry authored 7 years ago
  
  03cc2e3f
- Add GO correlation to St subclust QuSAGE · 8fd6047e
  Gervaise Henry authored 7 years ago
  
  8fd6047e
- Fix sc_LineageSubClust.R · eac456ca
  Gervaise Henry authored 7 years ago
  
  eac456ca