Improve setting of cell names #510
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* 'develop' of github.com:lazappi/seurat: (38 commits) Update .travis.yml Update .travis.yml fix hdf5r imports add option for variable gene selection add option in Read10X_h5 for ENSG names vs gene names run docs fixes 'implicit list embedding of S4 objects is deprecated' warning add function to read from hdf5 file Use scaler runif coeffRef(it.row(), it.col()) -> it.valueRef() Avoid unnecessary data.frame creation VlnPlot without jittered dots Fixes to 'show' method Minor syntactical changes (satijalab#12) Update plotting.R address PR satijalab#487 comments These changes are intended to fix issue 485 Place formula inside parallel loop Avoid Closure Reduce Memory Usage in RegressOutResid ...
Update cell names in all the different parts of a Seurat object
Only tests the fields that are set in pbmc_small so misse a couple of less common ones (kmeans and snn)
Also fix tabbing in RenameCells
* 'develop' of github.com:satijalab/seurat: install phate in travis_setup update NEWS merge travis setup scripts add travis_setup file fix hdf5 travis problems remove github deps setup file only exists in forked repo, include in .travis.yml for now locate setup file correctly reduce number of python versions download os appropriate miniconda miniconda might work better than apt try this a different way? apt doesn't have new enough version of python2, run tests with python3 instead? apt update to get latest python2 don't install numpy with apt appveyor parse error attempt to make CI pass add PHATE dimensionality reduction
* develop: install phate in travis_setup update NEWS merge travis setup scripts add travis_setup file fix hdf5 travis problems remove github deps setup file only exists in forked repo, include in .travis.yml for now locate setup file correctly reduce number of python versions download os appropriate miniconda miniconda might work better than apt try this a different way? apt doesn't have new enough version of python2, run tests with python3 instead? apt update to get latest python2 don't install numpy with apt appveyor parse error attempt to make CI pass add PHATE dimensionality reduction
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Merged develop to hopefully get Travis working after #511. |
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Thanks Luke! Very helpful function and should reduce confusion when analyzing multiple datasets. |
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No worries. Sorry for those couple of bugs, thanks for checking! |
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Hello, thanks |
andrewwbutler
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Jan 22, 2021
remove CheckMatrix(), to be moved into SeuratObject
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With more people combining datasets for analysis with
RunMultiCCAfixing duplicate cell names is becoming more of a problem as seen in #270, #290, #400, #505. To address this I have made the following changes:RenameCellsfunction that renames cells either by adding a prefix or replacing with a new vector of namesMergeSeuratto use the newRenameCellsfunction (to avoid duplication)add.cell.idsparameter toRunMultiCCAwhich appliesRenameCellsto each object inobject.list