| Get list the list of algorithms from a list of bicluster objects. | algohistogram |
| Apply a threshold to a bicluster similarity adjacency matrix or a co-occurrence adjacency matrix. | apply_threshold |
| Apply a threshold to a bicluster similarity adjacency matrix. | apply_threshold,bicluster_net-method |
| Apply a threshold to a co-occurrence adjacency matrix. | apply_threshold,cooccurrence_net-method |
| Count how often row/column elements occur in biclusters. | attr_overlap |
| Generate attribute specific co-occurance networks. | attribute_graph |
| Extract the class-wise degree of an adjacency matrix. | attributeConnector |
| Plot a heatmap of a bicluster | bicluster_heatmap |
| Plot a heatmap of a bicluster | bicluster_heatmap,bicluster,matrix-method |
| Convert Bicluster network to an igraph graph object | bicluster_net_to_igraph |
| Convert Bicluster network to an igraph graph object | bicluster_net_to_igraph,bicluster_net-method |
| A S4 class to store bicluster networks. | bicluster_net bicluster_net-class |
| Generate a bicluster network | bicluster_network |
| Convert a bicluster object to an acutal submatrix of the original matrix. | bicluster_to_matrix |
| Convert a bicluster object to an acutal submatrix of the original matrix. | bicluster_to_matrix,matrix,bicluster-method |
| A S4 class to store biclusters. | bicluster bicluster-class |
| Throw an error, if a matrix has not both row- and colnames. | check_names |
| Clean a list of biclusters, by returning only the valid ones, | clean_bicluster_list |
| Get the columnlengths for a list of bicluster objects. | colhistogram |
| Convert a co-occurence network to an igraph graph object | cooccurrence_net_to_igraph |
| Convert a co-occurrence to an igraph graph object | cooccurrence_net_to_igraph,cooccurrence_net-method |
| A S4 class to store co-occurence networks. | cooccurrence_net cooccurrence_net-class |
| Subsetting of R matrices within c++. | cpp_matrix_subsetting |
| Detect the number of elements in a list of biclusters. | detect_elements |
| Get the dimensions of a bicluster. | dim,bicluster-method |
| Compute distances between biclusters | distance_matrix |
| Convert communities into ensemble biclusters | ensemble_biclusters |
| Overlap of features/samples in different louvain communities | feature_louvain_overlap |
| Generate a co-occurence network | feature_network |
| Filter a list of bicluster objects, by erasing all biclusters, that do not fulfill the minimum number of rows and columns. Utilizes the function 'validate_bicluster'. | filter_bicluster_size |
| Filter biclusters based on a user defined filter function. | filter_biclusters |
| Filter a matrix | filter_matrix |
| Remove all biclusters from a list, that are identical or perfect subsets from each other. Additionally all invalid biclusters are removed (See 'validate_bicluster'). | filter_subsets |
| Generate a similarity network for a list of biclusters | full_graph |
| Get Adjacency matrix | get_adjacency |
| Get Adjacency matrix | get_adjacency,bicluster_net-method |
| Get Algorithms | get_algorithms |
| Get bicluster network algorithms | get_bic_net_algorithms |
| Get bicluster network algorithms | get_bic_net_algorithms,bicluster_net-method |
| Extract biclusters from different algorithms/packages | get_biclusters |
| Get louvain communities from a bicluster network | get_louvain_communities |
| Get louvain communities from a bicluster network | get_louvain_communities,bicluster_net-method |
| Get louvain communities from a co-occurrence network | get_louvain_communities,cooccurrence_net-method |
| Extract a list of bicluster objects from an akmbiclust biclustering object. | getAkmbiclustClusters |
| Get all biclusters from a Bi-Force output file. | getallBFClusters |
| Get a bicluster a Bi-Force output file | getBFCluster |
| Extract a list of bicluster objects from an BicARE biclustering object. | getBicAREbiclusters |
| Extract a list of bicluster objects from a biclust object. | getBiclustClusters |
| Extract a list of bicluster objects from an biclustpy output file. | getBiclustpyClusters |
| Extract a list of bicluster objects from an fabia biclustering object. | getFabiaClusters |
| Extract a list of bicluster objects from an isa2 biclustering object. | getIsaClusters |
| Extract QUBIC2 biclusters | getQUBIC2biclusters |
| Check, whether a matrix has row- and colnames. | has_names |
| Check if a bicluster is a subset (in rows AND columns) of identical to another bicluster. | is_subset_or_identical |
| Mouse brain lipidomics data | mouse_data |
| Count edges in an adjacency matrix using different cut-off thresholds. | network_edge_strength |
| Count edges in an adjacency matrix using different cut-off thresholds. | network_edge_strength_float |
| Get the number of biclusters, generated by the Bi-Force algorithm. | NoBFBiclusters |
| Node sizes for plotting bicluster networks. | node_size |
| Occurance matrix of data points in a list of biclusters | occurance_matrix |
| Occurance table of data points in a list of biclusters | occurance_table |
| Probability for an overlap of two samples. | p_overlap |
| Probability for an overlap of two dimensional samples | p_overlap_2d |
| Probability for an overlap higher or equal to the observed one of two dimensional samples | p_overlap_2d_higher |
| Probability for an overlap higher or equal to the observed one of two samples | p_overlap_higher |
| Plot a bicluster network colored by algorithms. | plot_algo_network |
| Plot a bicluster network with piecharts as nodes. | plot_piechart_bicluster_network |
| Plot a bicluster network | plot,bicluster_net,missing-method |
| Plot a co-occurrence network | plot,cooccurrence_net,missing-method |
| Randomize a matrix | randomize_matrix |
| Replace elements of an integer matrix. | replace_threshold |
| Replace values in an integer adjacency matrix. | replace_values |
| Replace values in a adjacency matrix. | replace_values_float |
| Get the rowlengths for a list of bicluster objects. | rowhistogram |
| Run the akmbiclust biclustering algorithm | run_akmbiclust |
| Run the Bimax biclustering algorithm | run_bimax |
| Run the CC biclustering algorithm | run_cc |
| Run the fabia biclustering algorithm | run_fabia |
| Run the isa biclustering algorithm | run_isa |
| Run the Plaid biclustering algorithm | run_plaid |
| Run the QUBIC biclustering algorithm | run_qubic |
| Run the Quest biclustering algorithm | run_quest |
| Run the spectral biclustering algorithm | run_spectral |
| Run the UniBic biclustering algorithm | run_unibic |
| Run the Xmotifs biclustering algorithm | run_xmotifs |
| Sample a list of biclusters. | sample_biclusters |
| Create a subset of biclusters based on a bicluster network | select_biclusters_from_bicluster_network |
| Create a subset of biclusters based on a bicluster network | select_biclusters_from_bicluster_network,bicluster_net,list-method |
| Add row-/colnames to a bicluster object. | set_bicluster_names |
| Add row-/colnames to a bicluster object. | set_bicluster_names,bicluster,matrix-method |
| Compute similarities between biclusters | similarity_matrix |
| Transpose a bicluster. Row and column slots will be changed. | transpose_bicluster |
| Indicates, whether a bicluster is valid. That means it needs at least one row and one column. | validate_bicluster |
| Save adjacency matrix as GraphML file | write_graphml |
| Write an R matrix to a file (In a Bi-Force or QUBIC2 readable format). | write_matrix |
| Make a vector of R indices compatible with c++ by substracting every element by one. | zero_subsetting |
