Commits · d8f09d03028897473923936cf23e7dd6ff3d01cf · BioCellGen-public / sirplus

Feb 14, 2020
- added eQTLEstimate function and eqtl params as an S4 parameters object · d8f09d03
  Christina Azodi authored 5 years ago
  
  d8f09d03
Feb 11, 2020
- add eQTL parameters S4 object information · e460328a
  Christina Azodi authored 5 years ago
  
  e460328a
- add eQTL parameters S4 object information · 4c64ef37
  Christina Azodi authored 5 years ago
  
  4c64ef37
Feb 04, 2020
- added vcf and gff example data · fa104838
  Christina Azodi authored 5 years ago
  
  fa104838
- update to use vcf and gff object instead of path · 945263d3
  Christina Azodi authored 5 years ago
  
  945263d3
- fixed nGroups not found bug · 547c1442
  Christina Azodi authored 5 years ago
  
  547c1442
- working version of splateQTL · 03ca12dc
  Christina Azodi authored 5 years ago
  
  03ca12dc
Jan 28, 2020
- first splat-eqtl commit · b30962ed
  Christina Azodi authored 5 years ago
  
  b30962ed
Jan 20, 2020
- testing · b642ef4d
  Christina Azodi authored 5 years ago
  
  b642ef4d
Oct 19, 2019
- addPer*QC() functions were renamed in scater 1.13.27 · a25de584
  Hervé Pagès authored 5 years ago
  
  a25de584
Oct 11, 2019
- Add missing documentation for sce in getCounts · 5bb38e0d
  Luke Zappia authored 5 years ago
  
  5bb38e0d
- Fix where simpleSimulate stores params · 99c8b9ac
  Luke Zappia authored 5 years ago
  
  Fixes #72
  99c8b9ac
- Check for counts assay when estimating from SCE · d6d7dba6
  Luke Zappia authored 5 years ago
  
  Fixes #82
  d6d7dba6
- Check spelling · 39b5b2a7
  Luke Zappia authored 5 years ago
  
  39b5b2a7
- Run checks · 55145cca
  Luke Zappia authored 5 years ago
  
  55145cca
Oct 10, 2019
- Rename Splotch to Kersplat · 4462511d
  Luke Zappia authored 5 years ago
  
  4462511d
- Add Splotch to listSims · d32da886
  Luke Zappia authored 5 years ago
  
  d32da886
- Document Splotch estimation functions · 66435625
  Luke Zappia authored 5 years ago
  
  66435625
Oct 09, 2019
- Document Splotch simulation functions · 9046703e
  Luke Zappia authored 5 years ago
  
  9046703e
Oct 01, 2019

Luke Zappia authored 5 years ago

* Change default cells.design to end of path
* Add experimental warning
* Avoid resetting cells.design

22c49d09

Sep 26, 2019
- Add doublets to SplotchSimulate · de7cf890
  Luke Zappia authored 5 years ago
  
  Might need a bit more work...
  de7cf890
Sep 24, 2019
- Add ambient expression and empty cells to Splotch · 790a051b
  Luke Zappia authored 5 years ago
  
  790a051b
Sep 19, 2019
- Rescale Phi when sampling in BASiCSSimulate · c8059ef5
  Luke Zappia authored 5 years ago
  
  c8059ef5
Sep 17, 2019
- Adjust BASiCSSimulate to match devel BASiCS · 7013aae2
  Luke Zappia authored 5 years ago
  
  7013aae2
Aug 29, 2019
- Add BCV adjustment to Splotch · 540b62d0
  Luke Zappia authored 5 years ago
  
  New exponential correction method for bcv.common estimates
  540b62d0
Aug 22, 2019
- Add density sampling option for means, lib sizes · 7d1fcd34
  Luke Zappia authored 5 years ago
  
  7d1fcd34
Aug 21, 2019
- Add violins to comparison plots · 84cdda8f
  Luke Zappia authored 5 years ago
  
  84cdda8f
- Replace library size log-norm with density · de1c10d9
  Luke Zappia authored 5 years ago
  
  Not sure if this this a good plan...
  de1c10d9
Aug 20, 2019
- Fix splotchEstimate example · c9b31a5f
  Luke Zappia authored 5 years ago
  
  c9b31a5f
- Replace sc_example_counts with mockSCE() · 55794d07
  Luke Zappia authored 5 years ago
  
  Tidy and improve examples
  55794d07
- Fix parameter passing in BASiCSEstimate · 06c83b52
  Luke Zappia authored 5 years ago
  
  Parameters were not being passed from the SingleCellExperiment method to the matrix method
  06c83b52
- Fix bug in diffSCEs QQ plots · b1fc4441
  Luke Zappia authored 5 years ago
  
  b1fc4441
- Add expression outliers to Splotch · dc9f6823
  Luke Zappia authored 5 years ago
  
  dc9f6823
Aug 14, 2019
- Fix bug in selectFit · a3d19d22
  Luke Zappia authored 5 years ago
  
  Handle missing (not NA) AIC values
  a3d19d22
Aug 13, 2019
- Add splotchEstimate function · dd9803d3
  Luke Zappia authored 5 years ago
  
  dd9803d3
Aug 08, 2019
- Simulate counts and organise functions · a4451854
  Luke Zappia authored 5 years ago
  
  a4451854
- Remove deprecated scater functions · 8276db58
  Luke Zappia authored 5 years ago
  
  Still some warnings from BASiCS...
  8276db58
Jul 17, 2019
- Add library size params and simulate cell means · 945343c7
  Luke Zappia authored 5 years ago
  
  945343c7
Jul 16, 2019
- Add paths parameters · effef406
  Luke Zappia authored 5 years ago
  
  effef406
- Add mean parameters · 61985cae
  Luke Zappia authored 5 years ago
  
  61985cae