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| aggregate_metadata | Performs aggregation on metadata contained in the association file. |
| aggregate_values_by_key | Aggregates matrices values based on specified key. |
| annotation_IS_vars | Names of the annotation variables for an integration matrix. |
| association_file_columns | Names of the columns in the association file. |
| as_sparse_matrix | Converts tidy integration matrices in the original sparse matrix form. |
| CIS_grubbs | Grubbs test for Common Insertion Sites (CIS). |
| CIS_volcano_plot | Trace volcano plot for computed CIS data. |
| clinical_relevant_suspicious_genes | Clinical relevant suspicious genes (for mouse and human). |
| comparison_matrix | obtain a single integration matrix from individual quantification matrices. |
| compute_abundance | Computes the abundance of every integration in the sample. |
| compute_near_integrations | Scans input matrix to find and merge near integration sites. |
| cumulative_count_union | Integrations cumulative count in time by sample |
| date_columns_coll | Possible choices for 'date_col' parameter. |
| date_formats | Possible choices for the 'dates_format' parameter in 'import_association_file', 'import_parallel_vispa2Matrices_interactive' and 'import_parallel_vispa2Matrices_auto'. |
| default_stats | A set of pre-defined functions for 'sample_statistics'. |
| generate_blank_association_file | Creates a blank association file. |
| generate_Vispa2_launch_AF | Creates a reduced association file for Vispa2 run, given project and pool |
| import_association_file | Import the association file from disk |
| import_parallel_Vispa2Matrices_auto | Import integration matrices based on the association file. |
| import_parallel_Vispa2Matrices_interactive | Import integration matrices based on the association file. |
| import_single_Vispa2Matrix | Import a single integration matrix from file |
| ISAnalytics | ISAnalytics: Analyze gene therapy vector insertion sites data identified from genomics next generation sequencing reads for clonal tracking studies |
| known_clinical_oncogenes | Known clinical oncogenes (for mouse and human). |
| mandatory_IS_vars | Names of mandatory variables for an integration matrix. |
| matching_options | Possible choices for the 'matching_opt' parameter. |
| quantification_types | Possible choices for the 'quantification_type' parameter. |
| realign_after_collisions | Re-aligns matrices of other quantification types based on the processed sequence count matrix. |
| reduced_AF_columns | Names of the columns of the association file to consider for Vispa2 launch. |
| remove_collisions | Identifies and removes collisions based on the sequence count matrix. |
| sample_statistics | Computes user specified functions on numerical columns and updates the metadata data frame accordingly. |
| separate_quant_matrices | Separate a multiple-quantification matrix into single quantification matrices. |
| threshold_filter | Filter data frames with custom predicates |
| top_integrations | Sorts and keeps the top n integration sites in a data frame. |
| unzip_file_system | A utility function to unzip and use example file systems included in the package |