Code

'debug' to 'master' for version 1.1.1#57

Code

Merged

farrellja merged 24 commits intomasterfarrellja/URD:masterfrom debugfarrellja/URD:debugCopy head branch name to clipboardApr 28, 2020

+1,253-373

Commits

Commits on Aug 6, 2019

• markersAUCPR calculates ratio

  

  jfarrell

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  59d72de

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• Fix labeling markersAUCPR

  

  jfarrell

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Commits on Aug 8, 2019

• markersAUCPR now objects auc.factor

  

  jfarrell

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Commits on Aug 16, 2019

• Added plotTreeHighlight and highlighting functions to plotTree

  

  jfarrell

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• Added additional customizations to plotDot and plotViolin

  

  jfarrell

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• Added a more evenly spaced color scale

  

  jfarrell

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• Corrected exp.fc which was not taking pseudocount of 1 into account when determining FC

  

  jfarrell

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• Added combineSmoothFit

  

  jfarrell

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• pseudotimeMovingWindow has option to have min pseudotime and cells simultaneously

  

  jfarrell

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• Bump 1.1.0.9002

  

  jfarrell

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Commits on Sep 16, 2019

• Fix bug introduced in aucprTestAlongTree introduced by updates to markersAUCPR

  

  jfarrell

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Commits on Sep 17, 2019

• Fixed log.effect.size filtering in markersAUCPR

  

  jfarrell

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Commits on Sep 24, 2019

• Added cells.min.walked to treeForceDirectedLayout

  

  jfarrell

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Commits on Oct 11, 2019

• Change symbol in NMFDoublets.R to facilitate installation.

  

  jfarrell

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Commits on Jan 15, 2020

• Use BiocManager for R >= 3.5

  farrellja

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Commits on Apr 7, 2020

• Explicitly call dip.test from diptest package.

  farrellja

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• Check no tips are specified without cells from loadTipCells.

  farrellja

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• If tips.use = NULL, extract them from @diff.data

  farrellja

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• Add parentheses

  farrellja

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Commits on Apr 8, 2020

• Limit ggraph to <2.0 until incompatibility is resolved.

  farrellja

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Commits on Apr 28, 2020

• Fix bug in treeLayout

  farrellja

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• ROxygen 6 > 7

  farrellja

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• Now tested with R 3.5 and R 3.6

  farrellja

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  1ca1b3c

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• Updated for version 1.1.1

  farrellja

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