Commits · master · Strand Lab / sc-TissueMapper

Jul 15, 2021
- Merge branch 'develop' into 'master' · f1e283fe
  Gervaise Henry authored 3 years ago
```
Develop

See merge request !6
```
  3.0.0
  
  f1e283fe
Jul 14, 2021
- Correct r.scripts · 8de3b69e
  Gervaise Henry authored 3 years ago
  
  8de3b69e
Jul 12, 2021
- Merge branch 'refactor' into 'develop' · ce300d01
  Gervaise Henry authored 3 years ago
```
Refactor

See merge request !5
```
  ce300d01
Mar 16, 2021
- Update qusage fncton · 1210457a
  Gervaise Henry authored 4 years ago
  
  1210457a
Mar 08, 2021
- Return lin id to cluster and add by-cell id after · 5dfeff3d
  Gervaise Henry authored 4 years ago
  
  5dfeff3d
Mar 02, 2021
- Change lin ID to single mode · a645e818
  Gervaise Henry authored 4 years ago
  
  a645e818
Mar 01, 2021
- Fix subset · a8a133ff
  Gervaise Henry authored 4 years ago
  
  a8a133ff
Feb 28, 2021
- Handle subsets if not all idents present · 82f83860
  Gervaise Henry authored 4 years ago
  
  82f83860
- Add mouse options and id lin by cluster · 8bf0a96b
  Gervaise Henry authored 4 years ago
  
  8bf0a96b
- Fix labels · 866f9a77
  Gervaise Henry authored 4 years ago
  
  866f9a77
Feb 22, 2021
- Add back ribo filter · 61083fb1
  Gervaise Henry authored 4 years ago
  
  61083fb1
- Change ribo lower cutoff to 10% and change thresh scale to 0-255 · 8ee45ed4
  Gervaise Henry authored 4 years ago
  
  8ee45ed4
- Revert nFeature lower cutoff to 200 · 36f0c834
  Gervaise Henry authored 4 years ago
  
  36f0c834
Feb 18, 2021
- Change nFeature lower cutoff to 1000 · 514afab2
  Gervaise Henry authored 4 years ago
  
  514afab2
Feb 12, 2021
- Fix stress/sample · a41f332f
  Gervaise Henry authored 4 years ago
  
  a41f332f
Feb 10, 2021
- Add hard cutoff for nCount and a bunch of small stuff · 7536f089
  Gervaise Henry authored 4 years ago
  
  7536f089
Feb 01, 2021
- Replace left over hardwired merge · 66e90556
  Gervaise Henry authored 4 years ago
  
  66e90556
- Fix merge param · 28e1dff3
  Gervaise Henry authored 4 years ago
  
  28e1dff3
- Double [] for merge arg · 21ef43a5
  Gervaise Henry authored 4 years ago
  
  21ef43a5
- Remove python load from bash · 92c1a74a
  Gervaise Henry authored 4 years ago
  
  92c1a74a
- Fix opt args · 7870fe92
  Gervaise Henry authored 4 years ago
  
  7870fe92
- Accept merge group from args · cbf5b349
  Gervaise Henry authored 4 years ago
  
  cbf5b349
- Significant edits · 7c902417
  Gervaise Henry authored 4 years ago
  
  7c902417
Dec 15, 2020
- Update human references (to lung) and increase scAlign setting · 11e5bd18
  Gervaise Henry authored 4 years ago
  
  11e5bd18
Nov 20, 2020
- Remove tsne plotting from ID · a0defb2a
  Gervaise Henry authored 4 years ago
  
  a0defb2a
Nov 19, 2020
- Up lin id res to 2 · 74ac6ca5
  Gervaise Henry authored 4 years ago
  
  74ac6ca5
- Remove tsne from stress figs · 6356ce6b
  Gervaise Henry authored 4 years ago
  
  6356ce6b
- Reduce n.neighbors for umap calc base on cell # · 667b5255
  Gervaise Henry authored 4 years ago
  
  667b5255
- Fix print umap only · 72d56204
  Gervaise Henry authored 4 years ago
  
  72d56204
- Stop caclulating tsne · 40b5287d
  Gervaise Henry authored 4 years ago
  
  40b5287d
- Add dynamic component calculation based on cell number (RAW) · 42ab2961
  Gervaise Henry authored 4 years ago
  
  42ab2961
- Remove IsoModes from thresh · f83b35f5
  Gervaise Henry authored 4 years ago
  
  f83b35f5
Nov 13, 2020
- Fix up mouse ID (use res 1.0 for lin) · f681be71
  Gervaise Henry authored 4 years ago
  
  f681be71
- Fix up mouse ID (use res 1.0 for lin) · 37869e73
  Gervaise Henry authored 4 years ago
  
  37869e73
Nov 12, 2020
- Add lower % ribo filter · e4c882e5
  Gervaise Henry authored 4 years ago
  
  e4c882e5
Nov 11, 2020
- Fix merge · 7a5d958b
  Gervaise Henry authored 4 years ago
  
  7a5d958b
- Split cutoff figs by sample names · c8a38d4a
  Gervaise Henry authored 4 years ago
  
  c8a38d4a
- Make sure sample names get set if loading from premade seurat objects · e2689018
  Gervaise Henry authored 4 years ago
  
  e2689018
Nov 10, 2020
- Specify assay and slot for QUSAGE · bb5be9b8
  Gervaise Henry authored 4 years ago
  
  bb5be9b8
Oct 30, 2020
- Fix bracketing · afb7560d
  Gervaise Henry authored 4 years ago
  
  afb7560d