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Submission to Bioconductor
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NAMESPACE
- Imported BiocFileCache package and R_user_dir() of tools package
- Exported new function conclusCacheClear()
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DESCRIPTION
- Removed LazyData: true.
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DataFormatting.R
- Added a caching system for retrieveFromGEO()
- Created conclusCacheClear() to delete the cache
- Updated documentation
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loadDataset.R
- Updated documentation
- Simplified nested "if" in loadDataset.R
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methods-normalization.R
- Modified the use of getBM to retrieve only genes of the count matrix (instead of the all database)
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test_setters.R/test_getters.R
- Modified documentation for loadDataOrMatrix()
- Simplified nested "if" in loadDataset.R
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test_loadData.R
- Adapted the unit tests to the new format of coldata and rowdata
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test_scRNAseq-methods.R
- Changed the experiment name to "Light_Experience"
- Used tempdir() for output directory
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inst
- Added inst/script to generate data on inst/extdata
- New data generated
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vignette
- Used tempdir() for output directory
- Specified other parameters in the first example of runCONCLUS for the very small dataset
- Replaced old paths by new ones
- Made the following significant changes
- Added an internal function .retrieveClustersNumberK to suggest the clusters number to use in lusterCellsInternal().
- Added suggestedClustersNumber slot in scRNAseq class to retrieve this suggested clusters number.
- Added accessors getSuggestedClustersNumber and setSuggestedClustersNumber.
- Updated all the objects used in examples and tests to have this slot.
- Made the following significant changes
- Add parameter removeNoSymbol in the method normalizeCountMatrix to filter genes doesn't have SYMBOL.
- clusterMarkers slot become topMarkers slot, accessors names change in the same way.0