Commits · 5141747e30b379ff4d82cfe81b18e408cce71a61 · BioCellGen-public / sirplus

Oct 01, 2019

Luke Zappia authored 5 years ago

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

5141747e

Sep 26, 2019
- Add doublets to SplotchSimulate · 09521792
  Luke Zappia authored 5 years ago
  
  Might need a bit more work...
  09521792
Sep 24, 2019
- Add ambient expression and empty cells to Splotch · 4d22ead2
  Luke Zappia authored 5 years ago
  
  4d22ead2
Sep 19, 2019
- Merge branch 'master' into splotch · 791c1419
  Luke Zappia authored 5 years ago
  
  * master: Rescale Phi when sampling in BASiCSSimulate Adjust BASiCSSimulate to match devel BASiCS
  791c1419
- Rescale Phi when sampling in BASiCSSimulate · 4aaf1aeb
  Luke Zappia authored 5 years ago
  
  4aaf1aeb
Sep 17, 2019
- Adjust BASiCSSimulate to match devel BASiCS · 053ea7ca
  Luke Zappia authored 5 years ago
  
  053ea7ca
Sep 09, 2019
- Merge branch 'master' into splotch · c92f6554
  Luke Zappia authored 5 years ago
  
  * master: Fix bug in NAMESPACE
  c92f6554
- Fix bug in NAMESPACE · d366e9a4
  Luke Zappia authored 5 years ago
  
  d366e9a4
Aug 29, 2019
- Add BCV adjustment to Splotch · 23992b03
  Luke Zappia authored 5 years ago
  
  New exponential correction method for bcv.common estimates
  23992b03
Aug 22, 2019
- Add density sampling option for means, lib sizes · 69ba7ee1
  Luke Zappia authored 5 years ago
  
  69ba7ee1
Aug 21, 2019
- Add violins to comparison plots · 8e396958
  Luke Zappia authored 5 years ago
  
  8e396958
- Replace library size log-norm with density · 9cb977b7
  Luke Zappia authored 5 years ago
  
  Not sure if this this a good plan...
  9cb977b7
Aug 20, 2019
- Fix splotchEstimate example · 6550c056
  Luke Zappia authored 5 years ago
  
  6550c056
- Merge branch 'master' into splotch · 5abc94a6
  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
  5abc94a6
- Rebuild pkgdown · 7986387c
  Luke Zappia authored 5 years ago
  
  7986387c
- Replace sc_example_counts with mockSCE() · d1fb46dc
  Luke Zappia authored 5 years ago
  
  Tidy and improve examples
  d1fb46dc
- Fix parameter passing in BASiCSEstimate · 41b26675
  Luke Zappia authored 5 years ago
  
  Parameters were not being passed from the SingleCellExperiment method to the matrix method
  41b26675
- Fix bug in diffSCEs QQ plots · b6a1405c
  Luke Zappia authored 5 years ago
  
  b6a1405c
- Add expression outliers to Splotch · 6895ab06
  Luke Zappia authored 5 years ago
  
  6895ab06
Aug 14, 2019
- Fix bug in selectFit · bb9e493b
  Luke Zappia authored 5 years ago
  
  Handle missing (not NA) AIC values
  bb9e493b
Aug 13, 2019
- Add splotchEstimate function · 7df8db07
  Luke Zappia authored 5 years ago
  
  7df8db07
Aug 08, 2019
- Simulate counts and organise functions · acd68b3a
  Luke Zappia authored 5 years ago
  
  acd68b3a
- Merge branch 'master' into splotch · d4a87c3a
  Luke Zappia authored 5 years ago
  
  * master: Remove deprecated scater functions
  d4a87c3a
- Remove deprecated scater functions · 8dcb671c
  Luke Zappia authored 5 years ago
  
  Still some warnings from BASiCS...
  8dcb671c
Jul 17, 2019
- Add library size params and simulate cell means · 2151840f
  Luke Zappia authored 5 years ago
  
  2151840f
Jul 16, 2019
- Add paths parameters · 7afee23b
  Luke Zappia authored 5 years ago
  
  7afee23b
- Add mean parameters · fbf8f8ec
  Luke Zappia authored 5 years ago
  
  fbf8f8ec
Jul 11, 2019
- Add SplotchParams object · 9bc0a897
  Luke Zappia authored 5 years ago
  
  Basic skeleton so far
  9bc0a897
Jun 13, 2019
- Update documentation · 8f5de2a2
  Luke Zappia authored 5 years ago
  
  View commits for tag v1.9.2 v1.9.2
  
  8f5de2a2
Jun 06, 2019
- Add variable gene correlation plot to compareSCEs · a1193734
  Luke Zappia authored 5 years ago
  
  a1193734
Jun 05, 2019
- Add the KS statistic to summariseDiff · a888e16a
  Luke Zappia authored 5 years ago
  
  View commits for tag v1.9.1 v1.9.1
  
  a888e16a
Jun 04, 2019
- Refactor summariseDiff · 5daced01
  Luke Zappia authored 5 years ago
  
  Split into functions, can now actually tell how it works...
  5daced01
- Set gam method for fitted lines in comp plots · 376979e4
  Luke Zappia authored 5 years ago
  
  376979e4
- Add suggested package checks to examples · 73e8e8d8
  Luke Zappia authored 5 years ago
  
  73e8e8d8
May 06, 2019
- Bioconductor 3.10 devel · 0ce11e5d
  Luke Zappia authored 5 years ago
  
  View commits for tag v1.9.0 v1.9.0
  
  0ce11e5d
- Bioconductor 3.9 release · daecb77d
  Luke Zappia authored 5 years ago
  
  View commits for tag v1.8.0 v1.8.0
  
  daecb77d
- Merge branch 'master' of git.bioconductor.org:packages/splatter · 31026931
  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
  31026931
May 03, 2019
- bump x.y.z versions to odd y after creation of RELEASE_3_9 branch · d7c2ee01
  Nitesh Turaga authored 5 years ago
  
  d7c2ee01
- bump x.y.z versions to even y prior to creation of RELEASE_3_9 branch · 0195bb5c
  Nitesh Turaga authored 5 years ago
  
  0195bb5c
Apr 18, 2019
- Add Splat parameters vignette · ff7f4ab7
  Luke Zappia authored 5 years ago
  
  Fix spelling
  View commits for tag v1.7.5 v1.7.5
  
  ff7f4ab7