NEWS

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clustSIGNAL 1.5.1

• Minor updates to vignette content.
• Added option for using externally generated low embeddings of smoothed data in the final clustering.
• Reduced the minimum number of centers used in bluster k-means from 5000 to 3000 in the initial and final clustering steps.
• Improved overall code for better scaling on large datasets.

clustSIGNAL 0.99.9 (2025-03-27)

• Minor updates to vignette content.

clustSIGNAL 0.99.8 (2025-03-21)

• The neighbourhood entropy calculation now includes the index cell's initial subcluster label. This is to ensure that distinct cells existing in otherwise completely homogeneous space are taken into account when measuring neighbourhood heterogeneity.
• Following additional parameter testing on simulated data, changed the default values of spread for Gaussian distribution (from 0.05 to 0.3) and clustering k (from 5 to 10), and recommended value of spread for exponential distribution (from 20 to 5).
• Moved all helper functions to the utilities.R file.
• Minor updates to the column names in which initial cluster and subcluster labels are stored after first clustering step.
• Updated the descriptions of all functions in the package.
• Improved the tutorial vignette content.

clustSIGNAL 0.99.7 (2025-01-08)

• Minor updates.
• Renamed the example dataset from example.RData to ClustSignal_example.RData
• Updated DESCRIPTION file to add bluster package version (>= 1.16.0) required to run ClustSIGNAL.

clustSIGNAL 0.99.6 (2024-12-11)

• Modified adaptiveSmoothing() function to improve its runtime.
• Improved the tutorial vignette content.
• Added step-by-step ClustSIGNAL run guide to the tutorial vignette.
• Removed the user parameter cells. The package automatically uses the column names of the input SpatialExperiment object as the cell ID.
• Added a cell id check - throws error if duplicates found among column names of input SpatialExperiment object.

clustSIGNAL 0.99.5 (2024-11-28)

• Fixed issue where absence of spatial coordinates was not throwing error at the beginning of the run.

clustSIGNAL 0.99.4 (2024-11-28)

• Corrected character check for output format type.

clustSIGNAL 0.99.0 (2024-09-19)

• Submitted to Bioconductor.

clustSIGNAL 0.00.3 (2024-10-31)

• Clustering parameter options added to package
• Initial and final clustering steps are now in separate functions
• Test units added to the package

clustSIGNAL 0.00.2 (2024-10-08)

• Updated parallel runs in smoothing function for faster runs