Commits · 790a051bb7c14af44b70f92688dc5f9b21505a40 · BioCellGen-public / sirplus

Sep 24, 2019
- Add ambient expression and empty cells to Splotch · 790a051b
  Luke Zappia authored 5 years ago
  
  790a051b
Sep 19, 2019
- Merge branch 'master' into splotch · 5819b94a
  Luke Zappia authored 5 years ago
  
  * master: Rescale Phi when sampling in BASiCSSimulate Adjust BASiCSSimulate to match devel BASiCS
  5819b94a
- 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
- Merge branch 'master' into splotch · 17b5a273
  Luke Zappia authored 5 years ago
  
  * master: Fix bug in NAMESPACE
  17b5a273
- 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
- Merge branch 'master' into splotch · 106bae48
  Luke Zappia authored 5 years ago
  
  * master: Rebuild pkgdown Replace sc_example_counts with mockSCE() Fix parameter passing in BASiCSEstimate Fix bug in diffSCEs QQ plots
  106bae48
- Rebuild pkgdown · 247158cf
  Luke Zappia authored 5 years ago
  
  247158cf
- 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
- Merge branch 'master' into splotch · af0fc55f
  Luke Zappia authored 5 years ago
  
  * master: Remove deprecated scater functions
  af0fc55f
- 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 06, 2019
- Add variable gene correlation plot to compareSCEs · 9f19d919
  Luke Zappia authored 5 years ago
  
  9f19d919
Jun 05, 2019
- Add the KS statistic to summariseDiff · 3ef183d0
  Luke Zappia authored 5 years ago
  
  3ef183d0
Jun 04, 2019
- Refactor summariseDiff · 17af980f
  Luke Zappia authored 5 years ago
  
  Split into functions, can now actually tell how it works...
  17af980f
- Set gam method for fitted lines in comp plots · ef217601
  Luke Zappia authored 5 years ago
  
  ef217601
- Add suggested package checks to examples · ebb9f4b4
  Luke Zappia authored 5 years ago
  
  ebb9f4b4
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
- Merge branch 'master' of git.bioconductor.org:packages/splatter · 67e536ff
  Luke Zappia authored 5 years ago
  
  * 'master' of git.bioconductor.org:packages/splatter: bump x.y.z versions to odd y after creation of RELEASE_3_9 branch bump x.y.z versions to even y prior to creation of RELEASE_3_9 branch
  67e536ff
May 03, 2019
- bump x.y.z versions to odd y after creation of RELEASE_3_9 branch · 64281acb
  Nitesh Turaga authored 5 years ago
  
  64281acb
- bump x.y.z versions to even y prior to creation of RELEASE_3_9 branch · 64d7e988
  Nitesh Turaga authored 5 years ago
  
  64d7e988
Apr 18, 2019
- Add Splat parameters vignette · 9657ff62
  Luke Zappia authored 5 years ago
  
  Fix spelling
  9657ff62
- Rename path.length to path.nSteps · 426139b9
  Luke Zappia authored 5 years ago
  
  426139b9
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