Canek 0.3.1

Changes

Sped up MNN pair finding: FindMnnPairs() scanned the full neighbor tables with which() for every cell and grew its result with repeated rbind() calls inside a loop, both of which scaled quadratically in cell count. Both are now near-linear, with no change in output (verified byte-identical against the previous implementation). Fuzzy() also no longer converts its correction matrix to a data.frame just to track a per-cell flag, which was much slower than tracking it as a plain vector. Together these give roughly a 2-4x speedup on real datasets, more on larger ones, since MNN search is repeated on every maxLoop pass.
Added an ncores parameter (CorrectBatches(), CorrectBatch(), GetMnnPairs(), and via ... on RunCanek()) to parallelize the two independent k-nearest-neighbor searches MNN pair finding requires. Defaults to 1 (fully sequential) — parallelism is opt-in only, since automatically detecting and using “available” cores could oversubscribe a shared cluster/HPC job’s actual allocation. Uses parallel::mclapply(), so ncores > 1 requires Linux/macOS (errors on Windows, and if more cores are requested than parallel::detectCores() reports, rather than silently falling back or capping). See the new Speed up batch correction with parallel processing vignette.

RunCanek() on Seurat objects now defaults to correctEmbeddings = TRUE: correction happens in PCA-embedding space instead of on gene expression directly, and the result is stored as a new "canek" dimensionality reduction rather than a new "Canek" assay. Code that reads assay = "Canek" after RunCanek() needs updating — use Embeddings(x, "canek") instead, or pass correctEmbeddings = FALSE to keep the original assay-based behavior.

pcaDim is now inferred automatically from an existing "pca" reduction on the object when not specified, instead of always defaulting to 50; falls back to 30 with a warning if no "pca" reduction exists.
When correctEmbeddings = TRUE and a "pca" reduction already exists, RunCanek() reuses it directly instead of recomputing one internally (new precomputedEmbeddings parameter on CorrectBatches()/ CorrectBatch()).
Added SCTransform support: RunCanek() auto-detects an existing "SCT" assay, and for correctEmbeddings = TRUE requires an existing "pca" reduction computed on properly reconciled data (see SCTransform documentation). Errors with guidance towards the reconciliation steps (SelectIntegrationFeatures() + PrepSCTIntegration()) are thrown.
Added a iterative-correction loop for correctEmbeddings = TRUE: new maxLoop/loopTol parameters (RunCanek() on Seurat objects defaults to maxLoop = 5) iterate the correction, feeding each pass’s result into the next, and stop early once further passes stop improving the correction.
Fixed a bug where clustering and the fuzzy logic step would error (subscript out of bounds) whenever correctEmbeddings = TRUE was used with pcaDim below 10.
Rewrote the Seurat vignette and added a new SCTransform vignette demonstrating the current default workflow for each normalization method. Pre-0.3.0 vignettes are archived under Previous versions.

Fix bug when using SCTransform. (#14)
Add BugReports and URL.(#13)
Relaxing tests to no consider the names attribute.(#12)
Refactor RunCanek() Seurat and SingleCellExperiment interfaces to preserve original objects.
Added integration.name argument to RunCanek() to customize the name of the integrated assay.