Changes in version 2.5.4 + adapt the code with markdown v1.6 Changes in version 2.5.3 + names are automatically added if `cola_opt$color_set_1` and `cola_opt$color_set_2` are specific without names. Changes in version 2.5.1 + In the rmarkdown, replace `message = FALSE` to `message = NA`. + use `%dorng%` for paralell computing Changes in version 2.1.1 + add hierarchical consensus partitioning Changes in version 2.0.1 + `predict_classes()`: support svm/random forest methods for class label prediction. Changes in version 1.9.1 + add `uniquely_high_in_one_group` method in `get_signatures()`. + add `compare_partitions()`. + parallel computing is implemented with foreach + doParallel Changes in version 1.9.0 + use row/column* family functions in `adjust_matrix()` to reduce the memory usage as well as improve the speed. Changes in version 1.5.6 + function to find best km for kmeans is improved. Changes in version 1.5.5 + add `enforce` argument in `get_signatures()`. + `subset` can be a vector of indices in `consensus_partition_by_down_sampling()`. Changes in version 1.5.3 + `predict_classes()` is speeded up 2x. + `get_signatures()`: add `top_signatures` argument to control the number of top signatures. Changes in version 1.5.2 + add a `DownSamplingConsensusPartition` class and corresponding methods. + add back `HierarchicalPartition` class and corresponding methods. Changes in version 1.5.1 + add a `predict_classes()` function. + add the cola analysis for Golub dataset as a data object in the package. + automatically install the "suggested" packages. Changes in version 1.3.2 + add a new vignette introducing functional enrichment. Changes in version 1.1.2 + improve documentations. Changes in version 1.1.1 + add `GO_enrichment()` and `map_to_entrez_id()`. + add `ncol()`/`nrow()`/`colnames()`/`rownames()`/`dim()` helper functions. + use `eulerr::euler()` to make the Euler diagram. + simplified the rules for deciding the best k. Changes in version 0.99.15 + support t-SNE and UMAP. Changes in version 0.99.14 + cola_report() supports `mc.cores`. Changes in version 0.99.13 + partition functions all support `mc.cores`. Changes in version 0.99.12 + implement get_consensus_matrix() by Cpp. + add regiester_NMF() and register_SOM(). Changes in version 0.99.9 + move TEMPLATE_DIR to `.onLoad()`. Changes in version 0.99.5 + reduce the number of packages loaded. + improve the package according to comments in https://github.com/Bioconductor/Contributions/issues/941#issuecomment-452728439 Changes in version 0.99.4 + fixed warnings in Rd files. Changes in version 0.99.3 + remove venneuler from DESCRIPTION. Changes in version 0.99.0 + Submitted to Bioconductor/