CIS_grubbs              Grubbs test for Common Insertion Sites (CIS).
CIS_grubbs_overtime     Compute CIS and Grubbs test over different time
                        points and groups.
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.
NGSdataExplorer         Launch the shiny application NGSdataExplorer.
aggregate_metadata      Performs aggregation on metadata contained in
                        the association file.
aggregate_values_by_key
                        Aggregates matrices values based on specified
                        key.
annotation_issues       Check for genomic annotation problems in IS
                        matrices.
as_sparse_matrix        Converts tidy integration matrices in the
                        original sparse matrix form.
association_file        Example of 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.
available_tags          All available tags for dynamic vars look-up
                        tables.
blood_lineages_default
                        Default blood lineages info
circos_genomic_density
                        Trace a circos plot of genomic densities.
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_is           Expands integration matrix with the cumulative
                        IS union over time.
date_formats            Possible choices for the 'dates_format'
                        parameter in 'import_association_file',
                        'import_parallel_vispa2Matrices_interactive'
                        and 'import_parallel_vispa2Matrices_auto'.
default_af_transform    Default transformations to apply to association
                        file columns.
default_iss_file_prefixes
                        Default regex prefixes for Vispa2 stats files.
default_meta_agg        Default metadata aggregation function table
default_rec_agg_lambdas
                        Defaults for column aggregations in
                        'compute_near_integrations()'.
default_report_path     Default folder for saving ISAnalytics reports.
                        Supplied as default argument for several
                        functions.
default_stats           A set of pre-defined functions for
                        'sample_statistics'.
enable_progress_bars    Enable global progress bars for ISAnalytics
                        functions.
export_ISA_settings     Export a dynamic vars settings profile.
fisher_scatterplot      Plot results of gene frequency Fisher's exact
                        test.
gene_frequency_fisher   Compute Fisher's exact test on gene
                        frequencies.
generate_Vispa2_launch_AF
                        Creates a reduced association file for a VISPA2
                        run, given project and pool
generate_blank_association_file
                        Create a blank association file.
generate_default_folder_structure
                        Generate a default folder structure, following
                        VISPA2 standards
import_ISA_settings     Import a dynamic vars settings profile.
import_Vispa2_stats     Import Vispa2 stats given the aligned
                        association file.
import_association_file
                        Import the association file from disk
import_parallel_Vispa2Matrices
                        Import integration matrices from paths in the
                        association file.
import_single_Vispa2Matrix
                        Import a single integration matrix from file
inspect_tags            Retrieve description of a tag by name.
integration_alluvial_plot
                        Alluvial plots for IS distribution in time.
integration_matrices    Example of imported multi-quantification
                        integration matrices.
is_sharing              Sharing of integration sites between given
                        groups.
iss_source              Find the source of IS by evaluating sharing.
known_clinical_oncogenes
                        Known clinical oncogenes (for mouse and human).
mandatory_IS_vars       Current dynamic vars specifications getters.
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.
pcr_id_column           Easily retrieve the name of the pcr id column.
proto_oncogenes         Data frames for proto-oncogenes (human and
                        mouse) amd tumor-suppressor genes from UniProt.
purity_filter           Filter integration sites based on purity.
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.
refGene_table_cols      Required columns for refGene file.
refGenes_hg19           Gene annotation files for hg19, mm9 and mm10.
remove_collisions       Identifies and removes collisions.
reset_mandatory_IS_vars
                        Resets dynamic vars to the default values.
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.
set_mandatory_IS_vars   Define custom dynamic vars.
set_matrix_file_suffixes
                        Sets the look-up table for matrix file
                        suffixes.
sharing_heatmap         Plot IS sharing heatmaps.
sharing_venn            Produce tables to plot sharing venn or euler
                        diagrams.
top_abund_tableGrob     Summary top abundant tableGrobs for plots.
top_cis_overtime_heatmap
                        Heatmaps for the top N common insertion sites
                        over time.
top_integrations        Sorts and keeps the top n integration sites
                        based on the values in a given column.
top_targeted_genes      Top n targeted genes based on number of IS.
transform_columns       Apply transformations to an arbitrary number of
                        columns.
