Canek

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.