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NEWS
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3.0.6:
+ Gene set collection update: TAM-related gene sets added
3.0.5:
+ Gene set collection update: CRC-metastasis-related gene sets added
3.0.4:
+ bugfix in parallel statistics when data matrix has low number of rows
3.0.3:
+ Vignette update
3.0.2:
+ Difference analysis core usage optimized
3.0.1:
+ Bugfixes in difference analysis and HTML scripts
3.0.0:
+ Optimization for large data set incl. massive parallelization of bottleneck functionalities; largedata.mode added
2.5.3:
+ PSF automatically skipped when too few KEGG pathway genes are covered
2.5.2:
+ Critical bugfix in PSF report sheets (error caused by wrong IDs extracted from xml files)
2.5.1:
+ Gene set collection update: Livermetastasis-related gene sets added
2.5.0:
+ PSF data and algorithm update according to PSF toolkit (https://github.com/hakobyansiras/psf)
2.4.2:
+ Gene set collection update: Livermetastasis-related gene sets added
2.4.1:
+ Gene set collection update: Martirosyan gene sets added
2.4.0:
+ Colorblind-save portraits introduced
2.3.1:
+ Gene set collection update: Konecny gene sets added
2.3.0:
+ spot.list.samples object removed
2.2.9:
+ Gene set collection updates & minor changes
2.2.8:
+ Gene set update: Tirosh molecular programs for multiple cell types and cancer
2.2.7:
+ Collection of multiple fixes and gene set updates
2.2.6:
+ Bugfix for module masks when empty spots were dropped
2.2.5:
+ Gene set collection update
2.2.4:
+ Gene set collection update
2.2.3:
+ Overexpression modules further enhanced; minor fixes for module overview maps; spot.borders() incorporated
2.2.2:
+ Overexpression modules are now always contiguous
2.2.1:
+ Gene set collection update
2.2.0:
+ oposSOM runs now in 'results' folder directly
2.1.9:
+ Bugfix in PAT group assignment with only one unique PAT
2.1.8:
+ Bugfix in sample SOM visualization with portraits
2.1.7:
+ Bugfixes in PAT assignment and group analysis statistics
2.1.6:
+ New gene sets added; minor fixes
2.1.5:
+ Module detection algorithms distributed over separated functions
2.1.4:
+ Revision of differential expression statistics and data structures
2.1.3:
+ PAT letters now ordered according to module activation frequency
2.1.2:
+ New color palettes implemented
2.1.1:
+ Calculation of p-values for gene set enrichment is activated by default
2.1.0:
+ PSF analysis module integrated into oposSOM
2.0.8:
+ Mapping of indata features to Ensembl IDs not limited to 1:1 anymore
2.0.7:
+ Bugfix for class(...) error occuring in R > 4.0.0
2.0.6:
+ Bugfixes for write.csv function, very long geneset file names and package version
2.0.5:
+ "note"-slot introduced to oposSOM environment (preferences) and html summary table
2.0.4:
+ Check implemented if over-/under-expression modules were detected. Check implemented if PAT class definition can be applied
2.0.3:
+ Check for detected singleton spot modules implemented
2.0.2:
+ csv output for international spreadsheet format
2.0.1:
+ Colored edges in sample correlation networks & minor fixes
2.0.0:
+ Great performance boost by implementation of parallel SOM calculation. "som" package dependence removed