Commits · 3365f4b0852cbb0b0caa0dd7d0919e4ead2a5332 · Strand Lab / sc-TissueMapper_Pr

Aug 31, 2018
- Fix Pd bash.script name · 3365f4b0
  Gervaise Henry authored 6 years ago
  
  3365f4b0
- Add bash.script to run Pd workflow · c9108026
  Gervaise Henry authored 6 years ago
  
  c9108026
- Remove depreciated D17 and D17+D27 bash.scripts · c9e3a9bb
  Gervaise Henry authored 6 years ago
  
  c9e3a9bb
- Remove depreciated D17 and D17+D27 workfolows · 71e4c555
  Gervaise Henry authored 6 years ago
  
  71e4c555
- Create Pd analysis workflow and fix some of the outputs · 80d84d6b
  Gervaise Henry authored 6 years ago
  
  80d84d6b
Aug 19, 2018
- Increase QuSAGE downsampleling to 50K · b7016e66
  Gervaise Henry authored 6 years ago
  
  b7016e66
Aug 16, 2018
- Update dws sc deg genesets · 84f10c2f
  Gervaise Henry authored 6 years ago
  
  84f10c2f
- Change stress cutoff from 95% to 90% · 0b7a1102
  Gervaise Henry authored 6 years ago
  
  0b7a1102
- Reduce max nodes from 50 to 45 for parallel processing · c4c43fd9
  Gervaise Henry authored 6 years ago
  
  c4c43fd9
Aug 15, 2018
- Change res for St to 0.3 and change cutoff for NE to 0.1% in D17 · 4115d3bc
  Gervaise Henry authored 6 years ago
  
  4115d3bc
- Fix NE score from using stress score · 161e2414
  Gervaise Henry authored 6 years ago
  
  161e2414
- Fix opt default for D2 --st · e86b3163
  Gervaise Henry authored 6 years ago
  
  e86b3163
- Fix downsampling logic for QuSAGE · 6d4794a3
  Gervaise Henry authored 6 years ago
  
  6d4794a3
Aug 08, 2018
- Change CCA: calculate 25, align 15 · 0edebb0a
  Gervaise Henry authored 6 years ago
  
  0edebb0a
Aug 06, 2018
- Let D17PrF only analysis load data from subfolder · 27575139
  Gervaise Henry authored 6 years ago
  
  0.1.0
  
  27575139
- Remove develop scripts · 64aaa55e
  Gervaise Henry authored 6 years ago
  
  64aaa55e
- Update README.md · 95cafb6f
  Gervaise Henry authored 6 years ago
  
  95cafb6f
Jul 15, 2018
- Add ridge and violins for top 10 NE DEGs and update DPrF's · 5de31f50
  Gervaise Henry authored 6 years ago
  
  5de31f50
Jul 14, 2018
- Updata dws.sc genesets · 402ce3fa
  Gervaise Henry authored 6 years ago
  
  402ce3fa
- Filter DEGs to only be a adj-p-value <=0.05, and loosen DEG criteria for NEs... · b6ebab19
  Gervaise Henry authored 6 years ago
```
Filter DEGs to only be a adj-p-value <=0.05, and loosen DEG criteria for NEs to genes present in 1% of cells and min of 1FC
```
  b6ebab19
- Change PCA analysis cutoof selection to CDF 95% · b3a4e775
  Gervaise Henry authored 6 years ago
  
  b3a4e775
Jul 13, 2018
- Previous commit was for DPrF.2, this one is the same to DPrF3 · 03e21f64
  Gervaise Henry authored 6 years ago
  
  03e21f64
- Change res to 0.2 in DPrF.3 and reduce QuSAGE downsample to 25,000 · 8c8e2730
  Gervaise Henry authored 6 years ago
  
  8c8e2730
- Only align 25 dims for 3CCA · e7838ceb
  Gervaise Henry authored 6 years ago
  
  e7838ceb
- Separate bash.scripts for 2 and 3 patient aggreagations · 9588554a
  Gervaise Henry authored 6 years ago
  
  9588554a
- Fix DPrF analysis to use correct CCA code and make separate r.scripts for 2... · 8482bc0d
  Gervaise Henry authored 6 years ago
```
Fix DPrF analysis to use correct CCA code and make separate r.scripts for 2 and 3 patient aggregation
```
  8482bc0d
Jul 12, 2018
- Fix downsample for QuSAGE · bf696392
  Gervaise Henry authored 6 years ago
  
  bf696392
- Add multi-CCA, fix RunTSNE and FindClusters to use cca.aligned, add Seurat Rename function · 222475c0
  Gervaise Henry authored 6 years ago
  
  222475c0
Jul 10, 2018
- Filter opposing pan-lineage markers from unique DEGs · 318a9ff7
  Gervaise Henry authored 6 years ago
  
  318a9ff7
Jul 09, 2018
- Update README.md · 1074c0ef
  Gervaise Henry authored 6 years ago
  
  1074c0ef
- Update README.md · 1a96b516
  Gervaise Henry authored 6 years ago
  
  1a96b516
- Update README.md · 849a6f69
  Gervaise Henry authored 6 years ago
  
  849a6f69
- Update readme.md · 641f5c1f
  Gervaise Henry authored 6 years ago
  
  641f5c1f
- Save empty analysis folder in git · 7008fdcf
  Gervaise Henry authored 6 years ago
  
  7008fdcf
Jul 08, 2018
- Add secondary analysis to DPr bash script · fc999941
  Gervaise Henry authored 6 years ago
  
  fc999941
- Remove depreciated bash scripts · fad1aca5
  Gervaise Henry authored 6 years ago
  
  fad1aca5
- Remove depreciated genesets · afa97489
  Gervaise Henry authored 6 years ago
  
  afa97489
- Remove depreciated R files · 6d788cd4
  Gervaise Henry authored 6 years ago
  
  6d788cd4
- Add pseudotime code · 01ee610c
  Gervaise Henry authored 6 years ago
  
  01ee610c
- Cleanup functions · d827f4e8
  Gervaise Henry authored 6 years ago
  
  d827f4e8