Man pages for calabrialab/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... |
| aggregate_values_by_key | Aggregates matrices values based on specified key. |
| annotation_issues | Check for genomic annotation problems in IS matrices. |
| association_file | Example of association file. |
| as_sparse_matrix | Converts tidy integration matrices in the original sparse... |
| available_outlier_tests | A character vector containing all the names of the currently... |
| 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. |
| CIS_grubbs | Grubbs test for Common Insertion Sites (CIS). |
| CIS_grubbs_overtime | Compute CIS and Grubbs test over different time points and... |
| 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... |
| compute_abundance | Computes the abundance for every integration event in the... |
| compute_near_integrations | Scans input matrix to find and merge near integration sites. |
| cumulative_count_union | Integrations cumulative count in time by sample |
| cumulative_is | Expands integration matrix with the cumulative IS union over... |
| date_formats | Possible choices for the 'dates_format' parameter in... |
| 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... |
| default_report_path | Default folder for saving ISAnalytics reports. Supplied as... |
| 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_blank_association_file | Create a blank association file. |
| generate_default_folder_structure | Generate a default folder structure, following VISPA2... |
| generate_Vispa2_launch_AF | Creates a reduced association file for a VISPA2 run, given... |
| HSC_population_plot | Plot of the estimated HSC population size for each patient. |
| HSC_population_size_estimate | Hematopoietic stem cells population size estimate. |
| import_association_file | Import the association file from disk |
| import_ISA_settings | Import a dynamic vars settings profile. |
| import_parallel_Vispa2Matrices | Import integration matrices from paths in the association... |
| import_parallel_Vispa2Matrices_auto | Import integration matrices from association file. |
| import_parallel_Vispa2Matrices_interactive | Import integration matrices from association file. |
| import_single_Vispa2Matrix | Import a single integration matrix from file |
| import_Vispa2_stats | Import Vispa2 stats given the aligned association 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... |
| ISAnalytics | ISAnalytics: Analyze gene therapy vector insertion sites data... |
| ISAnalytics-deprecated | Deprecated functions in package 'ISAnalytics'. |
| 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. |
| NGSdataExplorer | Launch the shiny application NGSdataExplorer. |
| outlier_filter | Filter out outliers in metadata, identified by the chosen... |
| 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... |
| 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... |
| reduced_AF_columns | Names of the columns of the association file to consider for... |
| refGenes_hg19 | Gene annotation files for hg19, mm9 and mm10. |
| refGene_table_cols | Required columns for refGene file. |
| 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... |
| separate_quant_matrices | Separate a multiple-quantification matrix into single... |
| 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. |
| threshold_filter | Filter data frames with custom predicates |
| 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... |
| top_targeted_genes | Top n targeted genes based on number of IS. |
| transform_columns | Apply transformations to an arbitrary number of columns. |
| unzip_file_system | A utility function to unzip and use example file systems... |
