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NEWS
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version 0.99.69 (2019-08-13)
- Added sctransform function to package
version 0.99.68 (2019-08-13)
- Fixed bug in ascend vignette
version 0.99.67 (2019-08-13)
- Updated documentation for datasets
version 0.99.66 (2019-08-09)
- Reduced number of genes in example datasets
- Edited gene marker selection in vignette
version 0.99.65 (2019-07-29)
- Reduced example data size
- Adapted functions to use smaller datasets
version 0.99.64 (2019-06-20)
- Reduced example datasize
- UMAP now uses PCA
version 0.99.4 (2019-06-19)
- Moved repository to powellgenomicslab
version 0.99.3 (2019-06-13)
- Addressed BiocCheck errors
- Introduced Rcpp and RcppArmadillo functionalities
- Moved to powellgenomicslab repository
version 0.9.9 (2019-03-01)
- Changed how objects are loaded EMSets via new EMSets
- Altered EMSet validation function to accomodate how slots are checked
- Changed SingleCellExperiment to EMSet conversion functions
version 0.9.8 (2019-01-22)
- Addressed R CMD check error messages
version 0.9.6 (2018-11-26)
- PCA check wasn't working correctly in the plotMDS function.
version 0.9.5 (2018-11-21)
- Changed calcVariance function to use less memory
- Reduced number of objects created by PCA function
version 0.9.4 (2018-11-20)
- Fixed issues with scran wrapper
version 0.9.2 (2018-11-07)
- Added parallel function to DESeq
- Fixed bug with DESeq
version 0.9.1 (2018-10-30)
- Resolved reoccuring error with runDESeq wrapper failing on some datasets.
- Resolved plotting issues associated with small datasets.
version 0.9.0 (2018-10-16)
- Updated CORE algorithm to now select high resolution plateau if it is more
stable than all clustering results generated within transition region.
- Fixed bug with scranNormalise and datasets generated from just expression
data.
- Updated normaliseBatches function to accept non-numeric batch labels
version 0.8.3 (2018-09-25)
- Fixed reclustering issue when CORE detects outliers in dataset
version 0.8.2 (2018-09-21)
- Fixed issue with installation related to faulty documentation
version 0.8.1 (2018-09-19)
- Bux fix for runCORE reclustering when outliers are found
version 0.8.0 (2018-09-05)
- Introduced variable genes functions
- Bug fixes associated with filtering functions
version 0.7.7 (2018-08-23)
- Fixed normaliseBatches function
- Added plotBatchNormQC function
version 0.7.6 (2018-08-17)
- Reverted SCORE algorithm name to CORE
- Major optimisations for large datasets
version 0.7.5 (2018-08-14)
- Optimisation for large datasets via sparse matrices
version 0.7.4 (2018-08-09)
- Updated documentation.
- Resolved issues with updateObject function.
- Removed build vignette reference from instructions.
version 0.7.3 (2018-08-08)
- Updated documentation. Resolved check conflicts.
version 0.7.2 (2018-08-07)
- Changed runCORE to runSCORE
- Added updateObject for converting old EMSets for compatability with the new
version of ascend.
version 0.7.0 (2018-08-02)
- Updated documentation of some functions.
- Updated base vignette.
version 0.6.8 (2018-07-20)
- Changed ConvertGeneAnnotation to convertGeneID and updated for new object.
version 0.6.7 (2018-07-17)
- Resolved repeat clustering issue with runCORE
version 0.6.6 (2018-07-17)
- Resolved bug with filterByOutliers
- Reassessed package dependencies
version 0.6.5 (2018-07-13)
- Updated documentation to reflect new functions.
- Resolved runTSNE issue.
version 0.6.0 (2018-07-11)
- Fixing installation issues.
version 0.6.0 (2018-07-11)
- Converted EMSet to SingleCellExperiment-inherited object.
- Restructured all functions to interact with new EMSet
- Added LRT function.
- Added DESeq2 wrapper.
version 0.5.2 (2018-05-16)
- Set stringAsFactors import in LoadCellRanger function to FALSE
version 0.5.0 (2018-04-30)
- Upgraded for compatibility with Bioconductor 3.7
- Removed functions related to the use of SCESets
version 0.3.5 (2018-04-05)
- Resolved R CMD check documentation warnings
- Changed Rmarkdown engine to multiformat
version 0.3.4 (2018-03-26)
- log2FoldChange is now reflective of Condition A rather than Condition B in
differential expression results
version 0.3.3 (2018-03-02)
- PlotStability now works properly for all resolutions
- Example datasets have been moved to another repository
- Ready for testing on other systems
version 0.2.9 (2018-01-31)
- Fixed size factor replacement in the intermediate Single Cell Experiment object used for scranNormalisation function
version 0.2.8 (2018-01-30)
- RunDiffExpression was still bugged - addressed condition subsetting
version 0.2.7 (2018-01-25)
- Fixed bug associated with RunDiffExpression - subsets were selected incorrectly
version 0.2.6 (2018-01-10)
- Fixed SubsetCondition
- Fixed RunDiffExpression for non-cluster differential expression function
- Updated ascend general vignette on how to use SubsetCondition correctly
version 0.2.5 (2018-01-09)
- Changed how RunDiffExpression compares datasets (subsetting of EMSets by user
is no longer required)
- Updated vignette to reflect recent changes
version 0.2.3 (2017-12-22)
- Debugged SCESet-associated scran functions
- Fixed % Variance label on PlotPCAVariance plot
- Changed SingleCellExperiment to Suggests
version 0.2.0 (2017-12-18)
- Upgraded references to scran/scater SCESet to SingleCellExpression objects.
- Added min.mean argument to scranNormalise function.
- Replaced PlotDendrogram’s kclust call with inputted clusters argument.
- Removed branch labels on PlotDendrogram with detailed legend.
- Replaced colour scale on PlotStabilityDendro with RColorBrewer’s paired palette.
- Updated required packages to reflect changes.
version 0.1.2 (2017-11-15)
- Added DESeq's estimateDispersions arguments to RunDiffExpression function
- Updated RGC_Tutorial.Rmd vignette to reflect updated functions.