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