NEWS

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sosta 1.3.4

• removed non working GitHub actions

sosta 1.3.3

• clarified difference between shapeMetric and totalShapeMetrics.
• updated FOV border characterization in vignette.

sosta 1.3.2

• changed minBoundaryDistances to allow for distance to FOV border characterization
• added "Structure boundary vs FOV boundary" section to vignette.

sosta 1.3.1

• added argument to simulate noise in createPointPatternTissue
• improved intensity value threshold estimation for reconstruction in .intensityThreshold

sosta 1.2.0

• Bioc 3.22 release version

sosta 1.1.4

• the argument imageCol is now not longer needed in reconstruction functions
• assingCellsToStructures for large datasets and 1 sample

sosta 1.1.3

• added sticker and preprint reference

sosta 1.1.2

• switch from GenomeInfoDb to new Seqinfo package

sosta 1.1.1

• added new function minCellTypeStructDist
• added possibility to reconstruct everything around an object (complement = TRUE)
• relaxed assertion of having at least two cells of each cell type in reconstruction to having at least one of one cell type

sosta 1.0.1

• fix problems in when assigning cell to structures

sosta 0.99.9

• Clarification of the transformation used in the diabetic islets vignette.

sosta 0.99.8

• Small changes in the vignettes and description.

sosta 0.99.7

• Small updates in vignettes.
• Updated news file for 0.99.6

sosta 0.99.6

• Improved parallel computation by reducing memory overhead by using data frames within mclapply instead of SpatialExperiment objects.
• Introduced new functions .SPE2df and .SPE2ppp to convert to different objects for reducing memory overhead.

sosta 0.99.5

• New Analysis Functions: Added assignCellsToStructures, calculateBorderMetrics, calculateCellTypeFractions, calculateDistanceToBorder, calculateDistanceToTissueRegion, and calculateTissueRegionFractions to improve spatial and structural analysis.
• Simulated data set: Introduced a new data set for testing and demonstrating package capabilities.
• Vignette update: Expanded documentation to include multi-sample and condition-based analysis.
• Bug fixes & optimisations: Addressed various issues and improved performance.
• Code cleanup: Enhanced readability, maintainability, and structure. Consistent use of camelCase for function arguments.

sosta 0.99.4

• Set number of cores to 1 to pass build on Windows.

sosta 0.99.3

Second round of review

• Changed required R version to >= 4.4.0
• Fixed typos
• Updated news file to match versions

sosta 0.99.2

Addressed first review

• Added R version and selective imports
• Functional programming to avoid code repetition
• Added unit tests and input checks
• Updated the vignette with installation info

sosta 0.99.1

Initial Bioconductor submission