CIS_grubbs              Grubbs test for Common Insertion Sites (CIS).
CIS_volcano_plot        Trace volcano plot for computed CIS data.
HSC_population_plot     Plot of the estimated HSC population size for
                        each patient.
HSC_population_size_estimate
                        Hematopoietic stem cells population size
                        estimate.
ISAnalytics             ISAnalytics: Analyze gene therapy vector
                        insertion sites data identified from genomics
                        next generation sequencing reads for clonal
                        tracking studies
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.
as_sparse_matrix        Converts tidy integration matrices in the
                        original sparse matrix form.
association_file_columns
                        Names of the columns in the association file.
available_outlier_tests
                        A character vector containing all the names of
                        the currently supported outliers tests that can
                        be called in the function outlier_filter.
blood_lineages_default
                        Default blood lineages info
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 for every integration
                        event in the input data frame.
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_iss_file_prefixes
                        Default regex prefixes for Vispa2 stats files.
default_meta_agg        Default metadata aggregation function table
default_stats           A set of pre-defined functions for
                        'sample_statistics'.
generate_Vispa2_launch_AF
                        Creates a reduced association file for Vispa2
                        run, given project and pool
generate_blank_association_file
                        Creates a blank association file.
import_Vispa2_stats     Import Vispa2 stats given the aligned
                        association file.
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
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.
outlier_filter          Filter out outliers in metadata, identified by
                        the chosen outlier test.
outliers_by_pool_fragments
                        Identify and flag outliers based on pool
                        fragments.
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
                        based on the values in a given column.
unzip_file_system       A utility function to unzip and use example
                        file systems included in the package
