- Jul 20, 2017
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Luke Zappia authored
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Luke Zappia authored
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- Jul 16, 2017
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Luke Zappia authored
Import SummarizedExperiment to avoid warnings
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Luke Zappia authored
* Add MAE, RMSE * Add scaled stats * Add ranks * Only return long table
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- Jul 04, 2017
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Luke Zappia authored
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Luke Zappia authored
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Luke Zappia authored
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Luke Zappia authored
* Add batch parameters * Replace groupCells with group.prob
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- Jul 03, 2017
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Luke Zappia authored
Now estimates number of each gene type
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- May 24, 2017
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Luke Zappia authored
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- Apr 25, 2017
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hpages@fhcrc.org authored
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/splatter@129128 bc3139a8-67e5-0310-9ffc-ced21a209358
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- Apr 14, 2017
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l.zappia authored
* master: Version 0.99.15 Remove dropout.present estimation Add limits to zeros plots Adjust default splat DE fac params Add BPPARAM to scDDSimulate Add summariseDiff function From: Luke Zappia <lazappi@users.noreply.github.com> git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/splatter@128698 bc3139a8-67e5-0310-9ffc-ced21a209358
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Luke Zappia authored
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Luke Zappia authored
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Luke Zappia authored
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- Mar 28, 2017
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l.zappia authored
* master: Version 0.99.14 Add panel function to vignette Change var plot scale Run checks Update panel functions Add makeOverallPanel function Add makeDiffPanel function Add options to comparison plots From: Luke Zappia <lazappi@users.noreply.github.com> git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/splatter@127789 bc3139a8-67e5-0310-9ffc-ced21a209358
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Luke Zappia authored
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Luke Zappia authored
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Luke Zappia authored
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Luke Zappia authored
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- Mar 27, 2017
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Luke Zappia authored
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- Mar 25, 2017
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l.zappia authored
* master: Version 0.99.13 Run checks Update Lun2 documentation Modify Lun2Params to use data.frame From: Luke Zappia <lazappi@users.noreply.github.com> git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/splatter@127694 bc3139a8-67e5-0310-9ffc-ced21a209358
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Luke Zappia authored
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- Mar 22, 2017
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l.zappia authored
* master: Version 0.99.12 Run checks Warn if bcv.df is infinite Update addFeatureStats col names Update progress message Switch to boxplots in compareSCESets Change Lun2 nGenes estimate Add diffSCESets to vignette Add diffSCESets function From: Luke Zappia <lazappi@users.noreply.github.com> git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/splatter@127605 bc3139a8-67e5-0310-9ffc-ced21a209358
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Luke Zappia authored
Make it clear which are added by Splatter
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Luke Zappia authored
Drawing quantiles in violins was causing an error
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Luke Zappia authored
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Luke Zappia authored
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- Mar 20, 2017
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l.zappia authored
* master: Version 0.99.11 Run checks Fix mean-zeros scale Make lun2Estimate parallel Allow non-interger Lun 2 lib sizes Fix dropout eta From: Luke Zappia <lazappi@users.noreply.github.com> git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/splatter@127511 bc3139a8-67e5-0310-9ffc-ced21a209358
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Luke Zappia authored
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Luke Zappia authored
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- Mar 07, 2017
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l.zappia authored
* master: Version 0.99.10 Remove out.loProb from vignette Update default Splat parameters Remove out.loProb parameter Update estimation procedure From: Luke Zappia <lazappi@users.noreply.github.com> git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/splatter@127213 bc3139a8-67e5-0310-9ffc-ced21a209358
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Luke Zappia authored
Decided it was unnecessary
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Luke Zappia authored
* Winsorize means * Only high outliers * Scale edgeR dispersion
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- Feb 02, 2017
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l.zappia authored
* master: Bump version number Update scDD reference Add addGeneLengths to vignette Add addGeneLengths tests Add addGeneLengths function Update Roxygen version Update README Add bioc-devel to Travis From: Luke Zappia <lazappi@users.noreply.github.com> git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/splatter@126415 bc3139a8-67e5-0310-9ffc-ced21a209358
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Luke Zappia authored
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Luke Zappia authored
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Luke Zappia authored
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- Jan 23, 2017
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l.zappia authored
* master: (123 commits) Fix non-linear path factors Bump verison number Set some examples to not run to save check time Initalise scDatEx to avoid NOTE Tidy up and bump version Replace 1:x Remove splatter.Rproj Add more detail about counts matrix Add installation to vignette Set R_TESTS environment Bump version to start build splatter 0.99.3 Updata scDDEstimate Add condition parameter Modify SCDDParams to take SummarizedExperiment Add logo to vignettes directory Remove scDD github remote Update to R-devel Address Bioconductor build warnings, notes Prepare for Bioconductor submission ... From: Luke Zappia <lazappi@users.noreply.github.com> git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/splatter@126081 bc3139a8-67e5-0310-9ffc-ced21a209358
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