Add num.threads= to all neighbor-based methods, to be passed to BiocNeighbors.
Parallelize the SNN graph construction in makeSNNGraph().
Corrected calculation of the ratio matrix in pairwiseRand() when adjusted=TRUE,
so that ratios have an upper bound of 1.
Previously zero-weight edges are now assigned a nominal positive weight in makeSNNGraph().
Added MbkmeansParam() to wrap mini-batch k-means from mbkmeans.
Added SOMParam() to wrap self-organizing map implementation from kohonen.
Added AffinityParam() to wrap the affinity propagation code from apcluster.
Added DbscanParam() to provide a custom DBSCAN implementation with automatic eps choice.
Added PamParam() to wrap the PAM implementation from cluster.
Added ClaraParam() to wrap the CLARA implementation from cluster.
Added AgnesParam() to wrap the agglomerative nesting method from cluster.
Added DianaParam() to wrap the divisive analysis method from cluster.
Added clusterSweep() to easily perform parameter sweeps via clusterRows().
Added linkClusters() to find relationships between clusters in different clusterings.
Added compareClusterings() to compute similarities between multiple clusterings.
Added nestedClusters() to quantify the degree of nesting across two clusterings.
Moved objects into objects$kmeans for KmeansParam() when full=TRUE.
Moved objects into objects$hclust for HclustParam() when full=TRUE.
Added clusterRMSD() to compute the root-mean-squared-deviation for each cluster.
New package bluster for modular clustering in Bioconductor packages.