Commits · 874de5604c23200ae1287c3989c16afa11bd7ce1 · Strand Lab / sc-TissueMapper_Pr

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- Remove outdated (non-SubClust) QuSAGE .R files · b8fa588e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
Mar 17, 2018
- Fix sc_Demultiplex.R from previous commit and fix QuSAGE Epi+St SubClust · 41748578
  Gervaise Henry authored 7 years ago
  
  41748578
- Fix sc_Demultiplex.R to be run default Pr project and update bash script · c1c1d51d
  Gervaise Henry authored 7 years ago
  
  c1c1d51d
- Remove test bash script · 6eff59b3
  Gervaise Henry authored 7 years ago
  
  6eff59b3
- Remove out of date subcluster QuSAGE · 5cc9e1f1
  Gervaise Henry authored 7 years ago
  
  5cc9e1f1
- Finalize code for lineage subclustering and QuSAGE · 2096510b
  Gervaise Henry authored 7 years ago
  
  2096510b
- Merge branch 'master' of git.biohpc.swmed.edu:StrandLab/sc-TissueMapper_Pr... · 1838a861
  Gervaise Henry authored 7 years ago
```
Merge branch 'master' of git.biohpc.swmed.edu:StrandLab/sc-TissueMapper_Pr into test.LineageSubClust_branch
```
  1838a861
Mar 14, 2018
- Add files missing from previous commit · 438822c4
  Gervaise Henry authored 7 years ago
  
  438822c4
- Add test code for QuSAGE on sub-clustering *still needs to be cleaned up before merging* · f581c1ed
  Gervaise Henry authored 7 years ago
  
  f581c1ed
Mar 12, 2018
- Fix formatting in README.md · c743dd80
  Gervaise Henry authored 7 years ago
  
  c743dd80
- Ignore .vscode folder · 0f9da75c
  Gervaise Henry authored 7 years ago
  
  0f9da75c
Mar 08, 2018
- Fix sample name error in sc_Demultiplex.R · b5c34682
  Gervaise Henry authored 7 years ago
  
  b5c34682
Mar 05, 2018
- Update README.md (link DWS Stress and NE genesets) · ccbb5d14
  Gervaise Henry authored 7 years ago
  
  ccbb5d14
- Finalize test code for lineage sub-clustering *still needs to be cleaned up before merging* · 726ec513
  Gervaise Henry authored 7 years ago
  
  726ec513
- add sc_LineageSubClust.R test script · b0cefef1
  Gervaise Henry authored 7 years ago
  
  b0cefef1
- Update README.md (Add lab info and update some formatting) · 71085fe9
  Gervaise Henry authored 7 years ago
  
  71085fe9
- Convert all png outputs to postscript .eps format · 9da57871
  Gervaise Henry authored 7 years ago
  
  9da57871
Feb 28, 2018
- Change to use 256Gb partition in bash script · 30e73d98
  Gervaise Henry authored 7 years ago
  
  30e73d98
- sc_DEG: save as .txt, save all DEGs in .Rda · 9ba785d1
  Gervaise Henry authored 7 years ago
  
  9ba785d1
- sc_DEG: change cairo to quartz in heatmaps, remove antialiassing from... · 99dcd5cb
  Gervaise Henry authored 7 years ago
```
sc_DEG: change cairo to quartz in heatmaps, remove antialiassing from violin/ridge plots, select unique DEGs for pops and plot aggregated dot plot and save as .txt, save all DEGs in .Rda
```
  99dcd5cb
Feb 27, 2018
- Add table for raw cell #'s for FACS pops · ce0cff61
  Gervaise Henry authored 7 years ago
  
  ce0cff61
- QuSAGE all clusters, store Cor.tables from QuSAGE.Lineage/Epi/St in... · 84a5e333
  Gervaise Henry authored 7 years ago
```
QuSAGE all clusters, store Cor.tables from QuSAGE.Lineage/Epi/St in cumulative.RData, reorder sub-cluster labels
```
  84a5e333
Feb 24, 2018
- Fix Cor.Table generation with anticorrelated clusters in sc_QuSAGE.Epi · bf6e4be6
  Gervaise Henry authored 7 years ago
  
  bf6e4be6
Feb 23, 2018
- Replace line 154 of sc_QuSAGE.Lineage.R removed in 8d47b5bb , labels lineage · 09678b47
  Gervaise Henry authored 7 years ago
  
  09678b47
- Fix Lineage cluster ordering · 34b3bb6b
  Gervaise Henry authored 7 years ago
  
  34b3bb6b
- Fix QuSAGE.Lineage+Epi to better handle lineage ambiguous (?) populations · 8d47b5bb
  Gervaise Henry authored 7 years ago
  
  8d47b5bb
Feb 21, 2018
- Add to .gitignore *~ to ignore open files · 6b3117fe
  Gervaise Henry authored 7 years ago
  
  6b3117fe
- Add garbage collection before Seurat-FindClusters commands in... · 44af3d5e
  Gervaise Henry authored 7 years ago
```
Add garbage collection before Seurat-FindClusters commands in sc_PC.Score.Stress.R and sc_Cluster.R because of memory errors with large experiments
```
  44af3d5e
Feb 16, 2018
- Change opt label for DWS NE markers · 6bd04092
  Gervaise Henry authored 7 years ago
  
  6bd04092
- Fix figure output folder in LGEA.Epi · ebde05d1
  Gervaise Henry authored 7 years ago
  
  ebde05d1
Feb 15, 2018
- Revert "Update bash.scripts and r.scripts to use R 3.4.1" · 09db6a01
  Gervaise Henry authored 7 years ago
```
This reverts commit 295a0dcf.
```
  09db6a01
Feb 13, 2018
- Fixed folder references for QuSAGE Epi + LGES.St & changed output folder for Tables · bc4714cd
  Gervaise Henry authored 7 years ago
  
  bc4714cd