Man pages for duohongrui/simutils
Common functions used in data simulation and evaluation
| add_class | Add A New Class |
| add_data_to_model | Add Gene Expression Data to Model |
| authors_definition | Authors information |
| cal_cor_dist | Calculate the Correlation Between Geodesic Distances |
| calculate_batch_properties | Calculate Batch Quantifying Metrics |
| calculate_CDI | Calculate Clustering Deviation Index (CDI) |
| calculate_CH_index | Calculate Calinski-Harabasz Index |
| calculate_cluster_properties | Summarize the Ability of Simulating Clusters |
| calculate_connectivity | Calculate Connectivity |
| calculate_DB_index | Calculate Davies-Bouldin Index |
| calculate_DEGs_properties | Summarize the Ability of Simulating DEGs |
| calculate_dunn | Calculate Dunn Index |
| calculate_ROGUE | Calculate ROUGE Value Calculate entropy-based metric for... |
| calculate_silhouette | Calculate Average Silouette Width |
| calculate_trajectory_properties | Calculate Metrics for Comparison of Two Trajectories |
| calculate_traj_metrics | Calculate Four Metrics to Compare Two Trajectories |
| cell_properties | Calculate Cell Properties |
| change_parameters | Change parameters |
| change_scGAN_parameters | Change Parameters About scGAN |
| change_values_in_list | Change Values From a List |
| check_prior_info | Check Prior Information |
| check_python_installation | Check Python Installation |
| data_conversion | Convert Data Format |
| default_parameters | Default Parameters of Simulation Methods |
| fix_path | Fix Paths on Windows |
| gene_properties | Calculate Gene Properties |
| get_default_value | Get the Default Value |
| get_S4_values | Get Values From S4 Object |
| h5_to_r | Read An H5 File into R |
| hs_gene_length | Gene Length of Homo sapiens |
| is_define_parameters | Check Class of Parameter Objects |
| leaf_node_depth | Trace the Depths of All Leaf Nodes |
| list_docker_container | List the Containers Existed in Docker |
| make_trees | Convert An Expression Matrix into Tree Format |
| manuscript_definition | Manuscript Information |
| match_cells | Match Cells in Reference Data with Those in Simulation Data |
| meta_info | Define Meta Information of A Dataset |
| method_definition | Method information and introduction |
| mm_gene_length | Gene Length of Mus musculus |
| model_predict | Establish A Model And Predict Cell Identity Using DEGs |
| node_height_dis | Calculate the Discrepency of Nodes' Height |
| normalization_simutils | FPKM or TPM Normalization Method in simutils |
| param_Boolean | Define Logical Parameters |
| param_character | Define Character Parameters |
| param_dataframe | Define Dataframe Object Parameters |
| parameter_sets | Generate Parameter sets |
| param_integer | Define Integer Parameters |
| param_numeric | Define Numeric Parameters |
| param_others | Define Other Object Parameters |
| param_reference | Define Reference Dataset Parameters |
| param_vector | Define Vector Parameters |
| perform_DEA | Perform Differential Expression Analysis This function is... |
| proportionate | A Number Multiplies Proportions Under Limitations |
| random_seed | A Random Seed |
| scgan_data_conversion | Convert R Matrix to Python h5ad File |
| set_parameters | Set Paramters |
| start_cell | Define A Start Cell of A Trajectory |
| synthesize_cells | Synthesize Fake Cells |
| test_uni_distribution | Test if the p-value is Uniformly Distributed |
| time_string | A String of Time |
| true_DEGs_proportion | Proportion of Matched DEGs |
| write_h5files | Write R object to .h5 Files |
