Commits · 3f331ef0b02547d2a3394360c0d1e3fcfe9e2e01 · Strand Lab / sc-TissueMapper_Pr

Oct 02, 2018
- Add initial code for ds.aggr (CellRanger tSNE and K-clust=10) · 3f331ef0
  Gervaise Henry authored 6 years ago
  
  3f331ef0
Oct 01, 2018
- Merge branch 'develop' into 'master' · 25690b09
  Gervaise Henry authored 6 years ago
```
Merge develop into master

See merge request sc-TissueMapper_Pr!2
```
  1.0.0
  
  25690b09
- Merge branch 'FACS' into 'develop' · 8ca3e573
  Gervaise Henry authored 6 years ago
```
Merge FACS into Develop

See merge request sc-TissueMapper_Pr!1
```
  8ca3e573
- Fix cca hvg intersect · c88d11c4
  Gervaise Henry authored 6 years ago
  
  c88d11c4
Sep 28, 2018
- Update README.md · f372f6c0
  Gervaise Henry authored 6 years ago
  
  f372f6c0
- Add R & bash scripts for D27_FACS · e2ef9276
  Gervaise Henry authored 6 years ago
  
  e2ef9276
- Fix the name of 1 diy fig · 6663b617
  Gervaise Henry authored 6 years ago
  
  6663b617
- Fix lin subset if unknown present · 0a5e6878
  Gervaise Henry authored 6 years ago
  
  0a5e6878
- Fix lin subset if unknown present and re-tSNE St · 4e44d665
  Gervaise Henry authored 6 years ago
  
  4e44d665
- Make Lin identity with St+Unknown merge and diy figs · becb0f99
  Gervaise Henry authored 6 years ago
  
  becb0f99
- Add bash script to run D17_FACS · 361eae03
  Gervaise Henry authored 6 years ago
  
  361eae03
- Remove depreciated code · 8d2c9547
  Gervaise Henry authored 6 years ago
  
  8d2c9547
- Add code to analyze D17_FACS · 8bc6ee2f
  Gervaise Henry authored 6 years ago
  
  8bc6ee2f
Sep 25, 2018
- Fix QuSAGE x-axis and some diy cust cols · e1efc698
  Gervaise Henry authored 6 years ago
  
  e1efc698
Sep 24, 2018
- Remove some depreciated code · d2aadde2
  Gervaise Henry authored 6 years ago
  
  d2aadde2
- Update sc DWS DEGs · 53367009
  Gervaise Henry authored 6 years ago
  
  53367009
- Update analysis, cutoff for nGenes increase due to deeper seq, don't recluster... · 99423e5c
  Gervaise Henry authored 6 years ago
```
Update analysis, cutoff for nGenes increase due to deeper seq, don't recluster subcluster, change genesets to not use readxl
```
  99423e5c
Sep 04, 2018
- Add QuSAGE to mouse lineage from scRNA-Seq (Montoro et al) · 0f46f0cd
  Gervaise Henry authored 6 years ago
  
  0f46f0cd
Sep 02, 2018
- Update dws.sc genesets · be4fecde
  Gervaise Henry authored 6 years ago
  
  be4fecde
- Remove downsampling from pseudotime and fix · 57b870d1
  Gervaise Henry authored 6 years ago
  
  57b870d1
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