NEWS

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cola 2.5.4

• adapt the code with markdown v1.6

cola 2.5.3

• names are automatically added if 'cola_opt$color_set_1' and 'cola_opt$color_set_2' are specific without names.

cola 2.5.1

• In the rmarkdown, replace 'message = FALSE' to 'message = NA'.
• use '%dorng%' for paralell computing

cola 2.1.1

• add hierarchical consensus partitioning

cola 2.0.1

• 'predict_classes()': support svm/random forest methods for class label prediction.

cola 1.9.1

• add 'uniquely_high_in_one_group' method in 'get_signatures()'.
• add 'compare_partitions()'.
• parallel computing is implemented with foreach + doParallel

cola 1.9.0

• use row/column* family functions in 'adjust_matrix()' to reduce the memory usage as well as improve the speed.

cola 1.5.6

• function to find best km for kmeans is improved.

cola 1.5.5

• add 'enforce' argument in 'get_signatures()'.
• 'subset' can be a vector of indices in 'consensus_partition_by_down_sampling()'.

cola 1.5.3

• 'predict_classes()' is speeded up 2x.
• 'get_signatures()': add 'top_signatures' argument to control the number of top signatures.

cola 1.5.2

• add a 'DownSamplingConsensusPartition' class and corresponding methods.
• add back 'HierarchicalPartition' class and corresponding methods.

cola 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.

cola 1.3.2

• add a new vignette introducing functional enrichment.

cola 1.1.2

• improve documentations.

cola 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.

cola 0.99.15

• support t-SNE and UMAP.

cola 0.99.14

• cola_report() supports 'mc.cores'.

cola 0.99.13

• partition functions all support 'mc.cores'.

cola 0.99.12

• implement get_consensus_matrix() by Cpp.
• add regiester_NMF() and register_SOM().

cola 0.99.9

• move TEMPLATE_DIR to '.onLoad()'.

cola 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

cola 0.99.4

• fixed warnings in Rd files.

cola 0.99.3

• remove venneuler from DESCRIPTION.

cola 0.99.0

• Submitted to Bioconductor/