Commits · 2904b426303b191992f46198bebb8aebf9bd669c · BioCellGen-public / sirplus

Oct 11, 2019
- Check for counts assay when estimating from SCE · 2258278e
  Luke Zappia authored 5 years ago
  
  Fixes #82
  2258278e
- Run checks · 644e6d84
  Luke Zappia authored 5 years ago
  
  644e6d84
Oct 10, 2019
- Document Splotch estimation functions · 33fc6396
  Luke Zappia authored 5 years ago
  
  33fc6396
Oct 09, 2019
- Document Splotch simulation functions · 3370996d
  Luke Zappia authored 5 years ago
  
  3370996d
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
- 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
- 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
- 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
- Replace sc_example_counts with mockSCE() · d1fb46dc
  Luke Zappia authored 5 years ago
  
  Tidy and improve examples
  d1fb46dc
- 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
- 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
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
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
Apr 17, 2019

Fix issue with parameter order in setParams · d60addd0

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.

d60addd0

Apr 15, 2019

Fix splatSimulate group order · 6be78728

Luke Zappia authored 5 years ago

Fixes #66

Groups (and paths) were being simulted in alphanumeric rather than number
order. Fixed by making the Group column a factor.

6be78728

Dec 06, 2018
- Add ImmunoOncology biocViews tag · b809a81b
  Luke Zappia authored 6 years ago
  
  At request of Bioconductor core team
  View commits for tag v1.6.1 v1.6.1
  
  b809a81b
Nov 17, 2018
- Fix bugs in vignette · 1d2175fe
  Luke Zappia authored 6 years ago
  
  scater normalise renamed to normalize
  View commits for tag v1.7.1 v1.7.1
  
  1d2175fe
Oct 31, 2018
- bump x.y.z versions to odd y after creation of RELEASE_3_8 branch · d9ee402d
  vobencha authored 6 years ago
  
  d9ee402d
- bump x.y.z versions to even y prior to creation of RELEASE_3_8 branch · 27073d48
  vobencha authored 6 years ago
  
  27073d48
Oct 22, 2018
- Add WithSpike when calling BASiCS_MCMC · 3abb9fa7
  Luke Zappia authored 6 years ago
  
  View commits for tag v1.5.8 v1.5.8
  
  3abb9fa7
Oct 03, 2018
- Fix BASiCSEstimate tests · eb22e79d
  Luke Zappia authored 6 years ago
  
  eb22e79d
Sep 08, 2018
- remove useDevel mention · 97ce90ee
  LiNk-NY authored 6 years ago
  
  97ce90ee