SpatialEcoTyper 0.0.1

First release of SpatialEcoTyper.
- SpatialEcoTyper: SE discovery from a single sample
- MultiSpatialEcoTyper: Integrative analysis of SEs from multiple samples
- IntegrateSpatialEcoTyper: Integrative analysis of SEs from multiple samples
- RecoverSE: SE recovery
- nmfClustering: NMF clustering
- SpatialView: draw spatial map of the tissue
- HeatmapView: draw a heatmap
- CreatePseudobulks: create pseudobulk mixtures
- NMFGenerateW: train an NMF model for SE deconvolution from bulk expression profiles
- NMFGenerateWList: train cell-type specific NMF model for SE recovery

SpatialEcoTyper 0.0.2

Reduce memory usage by computing distance of spatial neighbors and not all pairwise distances

SpatialEcoTyper 0.0.3

Reduce memory usage by replacing Reduce() with loops
Add seeds to nmfClustering
Re-organize the documentation for integrative analysis
Test and refine all documentations

SpatialEcoTyper 0.0.4

Test Seurat v4.2, v4.4 and v5 for the analysis and add related notes: they lead to different embedding and clustering results, but show high consistency (ARI=0.7) for the demo.
Add more figures to the output directory for integrative analysis
Add hints about the training of SE recovery model: the demo is less robust due to limited number of cells used. The training data should be as comprehensive as possible.
Add minibatch option to SNF2 function to reduce memory usage
Add hints about memory usage and parallel processing

SpatialEcoTyper 0.0.5

Add filter.region.by.celltypes option to SpatialEcoTyper and MultiSpatialEcoTyper

SpatialEcoTyper 1.0.0

First release