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Commits on Oct 22, 2022

• Merge pull request campbio#381 from joshua-d-campbell/devel

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• Updated Matrix conversion calls to be compatible with Matrix v1.4-2

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• Updates to version number and NEWS

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• Fixed bug related to factors/integers for z/y cluster labels within internal functions

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Commits on May 29, 2022

• Fixed bug with altExp usage in plotting cell annotation code

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Commits on May 1, 2022

• Merge branch 'master' into devel

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Commits on Apr 30, 2022

• Version bump and update docs for BioC 3.15

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Commits on Apr 27, 2022

• Fixed display names in feature plot in report

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• Fix in the report to work with displayName.

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Commits on Apr 26, 2022

• bump x.y.z version to odd y following creation of RELEASE_3_15 branch

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• bump x.y.z version to even y prior to creation of RELEASE_3_15 branch

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Commits on Apr 14, 2022

• Fixed bug where sample labels were not stored correctly when using recurrsive split. Updated report to handle plotting of character cell annotations without trying to convert to numeric

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Commits on Apr 13, 2022

• Remove install commands in vignettes. Version bump

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• Updated plotRPC functions to use splines instead of rolling mean

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Commits on Apr 11, 2022

• Fixed bug in perplexity of celda_G where phi was being recalculated

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• Removed ability to subsample counts matrix when calculating perplexity. This will take a much larger update where theta, probability of each cell population in each sample, will need to be calculat…

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Commits on Apr 5, 2022

• merged from master

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Commits on Mar 31, 2022

• Fixed max overlap warnings with ggrepel in plotDimReduceCluster

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• Updated docs and news

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Commits on Mar 30, 2022

• Added BiocCheck to Git Actions and changed dependency in standard check

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• Minor decontX vignette update

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Commits on Mar 29, 2022

• Merge remote-tracking branch 'bioc/master' into devel

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• Updates to decontX vignette and minor change to a decontX plotting function

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Commits on Mar 28, 2022

• Merge branch 'devel' of https://github.com/campbio/celda into devel

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• Added subsampling parameters for perplexity calculation to recursive split functions

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Commits on Mar 27, 2022

• Merge pull request campbio#363 from yuan-yin-truly/devel

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Commits on Mar 25, 2022

• Moved Matrix and SingleCellExperiment to Depends to make sure these are loaded when using celda

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Commits on Mar 24, 2022

• Seurat retrieve count matrix

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• Add on Seurat integration

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• singleCellTK integration

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• Add integration with Seurat

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• Correct typo in vignette and stress background should only contain empty droplets

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Commits on Jan 16, 2022

• Merge pull request campbio#357 from yuan-yin-truly/background_input_for_any_class_bugfixing

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Commits on Jan 15, 2022

• Resolve merging conflict

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• Merge pull request campbio#356 from yuan-yin-truly/adding_background_batch

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