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

Merged
merged 24 commits into from
Apr 28, 2020
Merged

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

merged 24 commits into from
Apr 28, 2020

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farrellja
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jfarrell and others added 24 commits August 6, 2019 11:45
markersAUCPR calculates ratio
59d72de
Fix labeling markersAUCPR
157db9a
markersAUCPR now objects auc.factor
cfca0a6
Added plotTreeHighlight and highlighting functions to plotTree
a3a338d
Added additional customizations to plotDot and plotViolin
57e184d
Added a more evenly spaced color scale
d198d42
Corrected exp.fc which was not taking pseudocount of 1 into account w…
b2c03d5 
…hen determining FC
Added combineSmoothFit
eae1a5f
pseudotimeMovingWindow has option to have min pseudotime and cells si…
a5bbd27 
…multaneously
Bump 1.1.0.9002
44e3452
Fix bug introduced in aucprTestAlongTree introduced by updates to mar…
3e22ec7 
…kersAUCPR
Fixed log.effect.size filtering in markersAUCPR
f73010e
Added cells.min.walked to treeForceDirectedLayout
277a8e0
Change symbol in NMFDoublets.R to facilitate installation.
d9f8983
@farrellja
Use BiocManager for R >= 3.5
265200a
@farrellja
Explicitly call dip.test from diptest package.
6bfe044
@farrellja
Check no tips are specified without cells from loadTipCells.
f76016f
@farrellja
If tips.use = NULL, extract them from @diff.data
6bdc52c
@farrellja
Add parentheses
2d1c9ed
@farrellja
Limit ggraph to <2.0 until incompatibility is resolved.
3d982d4
@farrellja
Fix bug in treeLayout
3168d01
@farrellja
ROxygen 6 > 7
258efb9
@farrellja
Now tested with R 3.5 and R 3.6
1ca1b3c
@farrellja
Updated for version 1.1.1
125c829
@farrellja farrellja merged commit d465abc into master Apr 28, 2020
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@farrellja