NEWS

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oposSOM 2.4.2

• Gene set collection update: Livermetastasis-related gene sets added

oposSOM 2.4.1

• Gene set collection update: Martirosyan gene sets added

oposSOM 2.4.0

• Colorblind-save portraits introduced

oposSOM 2.3.1

• Gene set collection update: Konecny gene sets added

oposSOM 2.3.0

• spot.list.samples object removed

oposSOM 2.2.9

• Gene set collection updates & minor changes

oposSOM 2.2.8

• Gene set update: Tirosh molecular programs for multiple cell types and cancer

oposSOM 2.2.7

• Collection of multiple fixes and gene set updates

oposSOM 2.2.6

• Bugfix for module masks when empty spots were dropped

oposSOM 2.2.5

• Gene set collection update

oposSOM 2.2.4

• Gene set collection update

oposSOM 2.2.3

• Overexpression modules further enhanced; minor fixes for module overview maps; spot.borders() incorporated

oposSOM 2.2.2

• Overexpression modules are now always contiguous

oposSOM 2.2.1

• Gene set collection update

oposSOM 2.2.0

• oposSOM runs now in 'results' folder directly

oposSOM 2.1.9

• Bugfix in PAT group assignment with only one unique PAT

oposSOM 2.1.8

• Bugfix in sample SOM visualization with portraits

oposSOM 2.1.7

• Bugfixes in PAT assignment and group analysis statistics

oposSOM 2.1.6

• New gene sets added; minor fixes

oposSOM 2.1.5

• Module detection algorithms distributed over separated functions

oposSOM 2.1.4

• Revision of differential expression statistics and data structures

oposSOM 2.1.3

• PAT letters now ordered according to module activation frequency

oposSOM 2.1.2

• New color palettes implemented

oposSOM 2.1.1

• Calculation of p-values for gene set enrichment is activated by default

oposSOM 2.1.0

• PSF analysis module integrated into oposSOM

oposSOM 2.0.8

• Mapping of indata features to Ensembl IDs not limited to 1:1 anymore

oposSOM 2.0.7

• Bugfix for class(...) error occuring in R > 4.0.0

oposSOM 2.0.6

• Bugfixes for write.csv function, very long geneset file names and package version

oposSOM 2.0.5

• "note"-slot introduced to oposSOM environment (preferences) and html summary table

oposSOM 2.0.4

• Check implemented if over-/under-expression modules were detected. Check implemented if PAT class definition can be applied

oposSOM 2.0.3

• Check for detected singleton spot modules implemented

oposSOM 2.0.2

• csv output for international spreadsheet format

oposSOM 2.0.1

• Colored edges in sample correlation networks & minor fixes

oposSOM 2.0.0

• Great performance boost by implementation of parallel SOM calculation. "som" package dependence removed