Man pages for BioSok/omada
Machine learning tools for automated transcriptome clustering analysis
| clusteringMethodSelection | Method Selection through intra-method Consensus Partition... |
| clusterVoting | Estimating number of clusters through internal exhaustive... |
| feasibilityAnalysis | Simulating dataset and calculate stabilities over different... |
| feasibilityAnalysisDataBased | Simulating dataset based on existing dataset's dimensions,... |
| featureSelection | Predictor variable subsampling sets and bootstrapping... |
| geneSignatures | Generating the feature/gene signature per cluster |
| get_agreement_scores | Get a dataframe of partition agreement scores for a set of... |
| get_average_feature_k_stabilities | Get a dataframe of average bootstrap stabilities |
| get_average_stabilities_per_k | Get average stabilities for all numbers of clusters(k) |
| get_average_stability | Get the average stability(over all k) |
| get_cluster_memberships_k | Get cluster memberships for every k |
| get_cluster_voting_k_votes | Get k vote frequencies |
| get_cluster_voting_memberships | Get cluster memberships for every k |
| get_cluster_voting_metric_votes | Get a dataframe with the k votes for every index |
| get_cluster_voting_scores | Get a matrix with metric scores for every k and internal... |
| get_coefficient_dataset | Get a list of LASSO (regression analysis) coefficients of... |
| get_feature_selection_optimal_features | Get the optimal features |
| get_feature_selection_optimal_number_of_features | Get the optimal number of features |
| get_feature_selection_scores | Get a dataframe of average bootstrap stabilities |
| get_generated_dataset | Get the simulated dataset |
| get_internal_metric_scores | Get a matrix with metric scores for every k and internal... |
| get_max_stability | Get the maximum stability |
| get_metric_votes_k | Get a dataframe with the k votes for every index |
| get_optimal_features | Get the optimal features |
| get_optimal_memberships | Get a dataframe with the memberships of the samples found in... |
| get_optimal_number_of_features | Get the optimal number of features |
| get_optimal_parameter_used | Get the optimal parameter used |
| get_optimal_stability_score | Get the optimal stability score |
| get_partition_agreement_scores | Get a dataframe of partition agreement scores for a set of... |
| get_sample_memberships | Get a dataframe with the memberships of the samples found in... |
| get_signature_feature_coefs | Get a list of LASSO (regression analysis) coefficients of... |
| get_top30percent_coefficients | Plot of the highest 30 percentage of coefficients per cluster |
| get_vote_frequencies_k | Get k vote frequencies |
| omada | A wrapper function that utilizes all tools to produce the... |
| optimalClustering | Clustering with the optimal parameters estimated by these... |
| partitionAgreement | Partition Agreement calculation between two clustering runs |
| plot_average_stabilities | Plot the average bootstrap stabilities |
| plot_cluster_voting | Plot k vote frequencies |
| plot_feature_selection | Plot the average bootstrap stabilities |
| plot_partition_agreement | Plot of partition agreement scores |
| plot_signature_feature | Plot of the highest 30 percentage of coefficients per cluster |
| plot_top30percent_coefficients | Plot of the highest 30 percentage of coefficients per cluster |
| plot_vote_frequencies | Plot k vote frequencies |
| toy_gene_memberships | Cluster memberships for toy gene data for package examples |
| toy_genes | Toy gene data for package examples |
