TF_human                Data to extract human TF
associationList         Data to showcase scRNA and scATAC-seq
                        association
calculate_mean_per_list_df
                        calculate_mean_per_list_df
check_patterns          check_patterns
discretize              Discretize ChIP-Seq counts to simulate a binary
                        dataset
experimentalDesign      Retrieves the experimental design
is.declared             Check if a variable is declared.
make_association_dataframe
                        make_association_dataframe
make_cluster_patterns   make_cluster_patterns
match_gene_regulator    match_gene_regulator
match_gene_regulator_cluster
                        match_gene_regulator_cluster
mosim                   mosim
omicData                Set customized data for an omic.
omicResults             Retrieves the simulated data.
omicSettings            Retrieves the settings used in a simulation
omicSim                 Set the simulation settings for an omic.
plotProfile             Generate a plot of a feature's profile for one
                        or two omics.
random_unif_interval    random_unif_interval Function to call the C
                        code This function is a copy of the
                        'random_unif_interval' function from the
                        'SPARSim' package (v0.9.5), originally
                        developed by Giacomo Baruzzo, Ilaria Patuzzi,
                        Barbara Di Camillo (2020). The original package
                        is licensed under the GPL-3 license.
sampleData              Default data
sc_mosim                sc_mosim
sc_omicData             sc_omicData
sc_omicResults          sc_omicResults
sc_omicSettings         sc_omicSettings
sc_param_estimation     sc_param_estimation
scatac                  Data to test scMOSim
scrna                   Data to test scMOSim
shuffle_group_matrix    shuffle_group_matrix, Reorder cell
                        type-specific expression matrix during
                        co-expression simulation. Copied from ACORDE
                        (https://github.com/ConesaLab/acorde) to
                        facilitate stability and running within our
                        scripts This function is a slightly modified
                        copy of the 'shuffle_group_matrix' function
                        from the 'Acorde' package (v1.0.0), originally
                        developed by Arzalluz-Luque A, Salguero P,
                        Tarazona S, Conesa A. (2022). acorde unravels
                        functionally interpretable networks of isoform
                        co-usage from single cell data. Nature
                        communications 1828. DOI:
                        10.1038/s41467-022-29497-w. The original
                        package is licensed under the GPL-3 license.
simulate_coexpression   simulate coexpression
simulate_hyper          Simulate technical variability
sparsim_create_simulation_parameter
                        Create SPARSim simulation parameter
sparsim_estimate_intensity
                        Estimate SPARSIm "intensity" parameter
sparsim_estimate_library_size
                        Estimate SPARSim "library size" parameter
sparsim_estimate_parameter_from_data
                        Estimate SPARSim simulation parameter from a
                        given count table
sparsim_estimate_variability
                        Estimate SPARSim "variability" parameter
sparsim_simulation      Function to simulate a raw count table
