Commits · f83b35f5dd577756b053f055acbbf7134c8eb05c · Strand Lab / sc-TissueMapper

Nov 19, 2020
- Remove IsoModes from thresh · f83b35f5
  Gervaise Henry authored 4 years ago
  
  f83b35f5
Nov 12, 2020
- Add lower % ribo filter · e4c882e5
  Gervaise Henry authored 4 years ago
  
  e4c882e5
Nov 11, 2020
- 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 29, 2020
- More refactoring · 21032bfc
  Gervaise Henry authored 4 years ago
  
  21032bfc
Oct 22, 2020
- Add assay to FindNeighbors · fcfc7fa9
  Gervaise Henry authored 4 years ago
  
  fcfc7fa9
Oct 19, 2020
- Finalize stress removal before align · 14ae840e
  Gervaise Henry authored 4 years ago
  
  14ae840e
Oct 07, 2020
- Mod fitering/align anchors/pca numbers · e2110a4e
  Gervaise Henry authored 4 years ago
  
  e2110a4e
Aug 17, 2020
- Start refactor RUN · 087770ca
  Gervaise Henry authored 4 years ago
  
  087770ca
Jun 29, 2020
- Fix nCount lower threshold · 94067e3e
  Gervaise Henry authored 4 years ago
  
  94067e3e
Feb 16, 2020
- Change threshold code to match qc thresh · dbb4d204
  Gervaise Henry authored 5 years ago
  
  dbb4d204
- Fix QC filter · 447e05b8
  Gervaise Henry authored 5 years ago
  
  447e05b8
Feb 08, 2020
- Add NE and QuSAGE to mus DIY · d37d5534
  Gervaise Henry authored 5 years ago
  
  d37d5534
Jan 13, 2020
- Do percent.mito upper thresh with > max · 386058b6
  Gervaise Henry authored 5 years ago
  
  386058b6
Sep 22, 2019
- Fix dehash display · f259f6e2
  Gervaise Henry authored 5 years ago
  
  f259f6e2
Sep 21, 2019
- Add dehashing for muPr · 305c7585
  Gervaise Henry authored 5 years ago
  
  305c7585
Sep 20, 2019
- Change nCount filter to MinErrorI · f2fcee3e
  Gervaise Henry authored 5 years ago
  
  f2fcee3e
Sep 18, 2019
- Make lower cutoff for nCount with filtered cells · 24967dcc
  Gervaise Henry authored 5 years ago
  
  24967dcc
Sep 17, 2019
- Change nCount threshold to MinErrorI · 645e0d90
  Gervaise Henry authored 5 years ago
  
  645e0d90
- Fix id subclust clusters with only one ident · 41df73b3
  Gervaise Henry authored 5 years ago
  
  41df73b3
Sep 16, 2019
- Fix matrix · c918d449
  Gervaise Henry authored 5 years ago
  
  c918d449
- Revert to sparse matrix for shiny out · cdf63c25
  Gervaise Henry authored 5 years ago
  
  cdf63c25
- In shiny save, don't treat exp data as sparse · c9d38b61
  Gervaise Henry authored 5 years ago
  
  c9d38b61
- Finish shiny output for raw and id including deg · da218911
  Gervaise Henry authored 5 years ago
  
  da218911
Sep 10, 2019
- Add nCount_RNA low cutoff (also percent.ribo calc, but don't use for filter),... · 1e66398e
  Gervaise Henry authored 5 years ago
```
Add nCount_RNA low cutoff (also percent.ribo calc, but don't use for filter), and make filtering consecutive)
```
  1e66398e
Sep 05, 2019
- Change integrate from cca to rpca · 044a4370
  Gervaise Henry authored 5 years ago
  
  044a4370
Aug 14, 2019
- Rejigger thresholding · 1566d195
  Gervaise Henry authored 5 years ago
  
  1566d195
Aug 13, 2019
- Score stress cutoff to the right of the max · eb9c4542
  Gervaise Henry authored 5 years ago
  
  eb9c4542
Aug 12, 2019
- Remove intermodes from threshoding · 45406133
  Gervaise Henry authored 5 years ago
  
  45406133
Aug 11, 2019
- Only use samples which were sequenced deep, merge samples less than 750 cells b4 CCA · 407e9306
  Gervaise Henry authored 5 years ago
  
  407e9306
Jul 18, 2019
- Change clustering to use integrated assay · ad3d6d5f
  Gervaise Henry authored 5 years ago
  
  ad3d6d5f
Jul 17, 2019
- Use SCT instead of RNA for score · 4dce7aea
  Gervaise Henry authored 5 years ago
  
  4dce7aea
Jul 16, 2019
- Update cca with new Seurat recommendations · 7fd5e495
  Gervaise Henry authored 5 years ago
  
  7fd5e495
Jun 07, 2019
- Fix RenyiEntropy name · beda2bd4
  Gervaise Henry authored 5 years ago
  
  beda2bd4
Jun 06, 2019
- Change stress scoring cutoff to RenjiEntropy · 7188ef69
  Gervaise Henry authored 5 years ago
  
  7188ef69
Jun 05, 2019
- Make indevidual plots for filtered qc plots · 857c0bd9
  Gervaise Henry authored 5 years ago
  
  857c0bd9
- Fix cutoff scale/unscale · 0f7116a9
  Gervaise Henry authored 5 years ago
  
  0f7116a9
May 31, 2019
- BIG update: import samples independent, not aggr; change assays for different... · 7e42e192
  Gervaise Henry authored 5 years ago
```
BIG update: import samples independent, not aggr; change assays for different functions; partial cleanup of functions
```
  7e42e192
May 14, 2019
- Fix QC filtering · 1337e208
  Gervaise Henry authored 6 years ago
  
  1337e208