Commits · bd821d138618dcb8ecf5c8a61b7bab30cec1bbd5 · BioCellGen-public / sirplus

Dec 13, 2019
- Bioconductor 3.10 release · bd821d13
  Luke Zappia authored 5 years ago
  
  bd821d13
Oct 20, 2019
- Update NEWS.Rd · 37dd640e
  Luke Zappia authored 5 years ago
  
  37dd640e
- Update DESCRIPTION, NEWS for scater QC funcs · 21aa3e4f
  Luke Zappia authored 5 years ago
  
  21aa3e4f
Oct 16, 2019
- Bump version number · 6ac6cb98
  Luke Zappia authored 5 years ago
  
  6ac6cb98
- Update maintainer email · fd977b26
  Luke Zappia authored 5 years ago
  
  fd977b26
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
- 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
Sep 09, 2019
- Fix bug in NAMESPACE · f9607578
  Luke Zappia authored 5 years ago
  
  f9607578
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
- 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
Jul 11, 2019
- Add SplotchParams object · a98dad15
  Luke Zappia authored 5 years ago
  
  Basic skeleton so far
  a98dad15
Jun 13, 2019
- Update documentation · 3d43018f
  Luke Zappia authored 5 years ago
  
  3d43018f
Jun 05, 2019
- Add the KS statistic to summariseDiff · 3ef183d0
  Luke Zappia authored 5 years ago
  
  3ef183d0
May 06, 2019
- Bioconductor 3.10 devel · dc56b4c8
  Luke Zappia authored 5 years ago
  
  dc56b4c8
- Bioconductor 3.9 release · 687fd125
  Luke Zappia authored 5 years ago
  
  687fd125
Apr 18, 2019
- Add Splat parameters vignette · 9657ff62
  Luke Zappia authored 5 years ago
  
  Fix spelling
  9657ff62
Apr 17, 2019

Fix issue with parameter order in setParams · 4268bc15

Luke Zappia authored 5 years ago

Fixes #69

Checks for SpatParams caused errors if parameters weren't supplied in the right
order. Fixed by making setParams a method and reordering the update list
before setting parameters.

4268bc15