{ "_id": "6a103c3cacfb0bcc41c9bdd3", "Package": "ISAnalytics", "Title": "Analyze gene therapy vector insertion sites data identified from\ngenomics next generation sequencing reads for clonal tracking\nstudies", "Version": "1.23.0", "Date": "2025-07-21", "Authors@R": "c(\nperson(given = \"Francesco\",\nfamily = \"Gazzo\",\nrole = c(\"cre\"),\nemail = \"gazzo.francesco@hsr.it\",\ncomment = c(ORCID = \"0009-0000-4626-1386\")),\nperson(given = \"Giulia\",\nfamily = \"Pais\",\nrole = c(\"aut\"),\nemail = \"giuliapais1@gmail.com\",\ncomment = c(ORCID = \"0009-0005-5621-4803\")),\nperson(given = \"Andrea\",\nfamily = \"Calabria\",\nrole = c(\"aut\"),\nemail = \"calabria.andrea@hsr.it\"),\nperson(given = \"Giulio\",\nfamily = \"Spinozzi\",\nrole = c(\"aut\"),\nemail = \"spinozzi.giulio@hsr.it\"))", "Description": "In gene therapy, stem cells are modified using viral\nvectors to deliver the therapeutic transgene and replace\nfunctional properties since the genetic modification is stable\nand inherited in all cell progeny. The retrieval and mapping of\nthe sequences flanking the virus-host DNA junctions allows the\nidentification of insertion sites (IS), essential for\nmonitoring the evolution of genetically modified cells in vivo.\nA comprehensive toolkit for the analysis of IS is required to\nfoster clonal trackign studies and supporting the assessment of\nsafety and long term efficacy in vivo. This package is aimed at\n(1) supporting automation of IS workflow, (2) performing base\nand advance analysis for IS tracking (clonal abundance, clonal\nexpansions and statistics for insertional mutagenesis, etc.),\n(3) providing basic biology insights of transduced stem cells\nin vivo.", "License": "CC BY 4.0", "URL": "https://calabrialab.github.io/ISAnalytics,\nhttps://github.com//calabrialab/isanalytics,\nhttps://calabrialab.github.io/ISAnalytics/", "BugReports": "https://github.com/calabrialab/ISAnalytics/issues", "biocViews": "BiomedicalInformatics, Sequencing, SingleCell, CellBiology,\nFunctionalGenomics, DataImport", "Encoding": "UTF-8", "LazyData": "false", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "RdMacros": "lifecycle", "Config/testthat/edition": "3", "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev libssl-dev\nlibx11-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:53:33 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"concept": [ "Utilities" ], "topics": [ "comparison_matrix" ] }, { "page": "compute_abundance", "title": "Computes the abundance for every integration event in the input data frame.", "concept": [ "Analysis functions" ], "topics": [ "compute_abundance" ] }, { "page": "compute_near_integrations", "title": "Scans input matrix to find and merge near integration sites.", "concept": [ "Data cleaning and pre-processing" ], "topics": [ "compute_near_integrations" ] }, { "page": "cumulative_is", "title": "Expands integration matrix with the cumulative IS union over time.", "concept": [ "Analysis functions" ], "topics": [ "cumulative_is" ] }, { "page": "date_formats", "title": "Possible choices for the 'dates_format' parameter in 'import_association_file', 'import_parallel_vispa2Matrices_interactive' and 'import_parallel_vispa2Matrices_auto'.", "concept": [ "Import functions helpers" ], "topics": [ "date_formats" ] }, { "page": "default_af_transform", "title": "Default transformations to apply to association file columns.", "concept": [ "Import functions helpers" ], "topics": [ "default_af_transform" ] }, { "page": "default_iss_file_prefixes", "title": "Default regex prefixes for Vispa2 stats files.", "concept": [ "Import functions helpers" ], "topics": [ "default_iss_file_prefixes" ] }, { "page": "default_meta_agg", "title": "Default metadata aggregation function table", "concept": [ "Data cleaning and pre-processing" ], "topics": [ "default_meta_agg" ] }, { "page": "default_rec_agg_lambdas", "title": "Defaults for column aggregations in 'compute_near_integrations()'.", "topics": [ "default_rec_agg_lambdas" ] }, { "page": "default_report_path", "title": "Default folder for saving ISAnalytics reports. Supplied as default argument for several functions.", "topics": [ "default_report_path" ] }, { "page": "default_stats", "title": "A set of pre-defined functions for 'sample_statistics'.", "concept": [ "Analysis functions helpers" ], "topics": [ "default_stats" ] }, { "page": "enable_progress_bars", "title": "Enable global progress bars for ISAnalytics functions.", "concept": [ "Utilities" ], "topics": [ "enable_progress_bars" ] }, { "page": "export_ISA_settings", "title": "Export a dynamic vars settings profile.", "concept": [ "Utilities" ], "topics": [ "export_ISA_settings" ] }, { "page": "fisher_scatterplot", "title": "Plot results of gene frequency Fisher's exact test.", "concept": [ "Plotting functions" ], "topics": [ "fisher_scatterplot" ] }, { "page": "gene_frequency_fisher", "title": "Compute Fisher's exact test on gene frequencies.", "concept": [ "Analysis functions" ], "topics": [ "gene_frequency_fisher" ] }, { "page": "generate_blank_association_file", "title": "Create a 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"concept": [ "Plotting functions" ], "topics": [ "integration_alluvial_plot" ] }, { "page": "integration_matrices", "title": "Example of imported multi-quantification integration matrices.", "topics": [ "integration_matrices" ] }, { "page": "is_sharing", "title": "Sharing of integration sites between given groups.", "concept": [ "Analysis functions" ], "topics": [ "is_sharing" ] }, { "page": "iss_source", "title": "Find the source of IS by evaluating sharing.", "concept": [ "Analysis functions" ], "topics": [ "iss_source" ] }, { "page": "known_clinical_oncogenes", "title": "Known clinical oncogenes (for mouse and human).", "concept": [ "Plotting function helpers" ], "topics": [ "known_clinical_oncogenes" ] }, { "page": "mandatory_IS_vars", "title": "Current dynamic vars specifications getters.", "concept": [ "dynamic vars" ], "topics": [ "annotation_IS_vars", "association_file_columns", "iss_stats_specs", "mandatory_IS_vars", "matrix_file_suffixes", "vars_getters" ] }, { "page": "matching_options", "title": "Possible choices for the 'matching_opt' parameter.", "concept": [ "Import functions helpers" ], "topics": [ "matching_options" ] }, { "page": "NGSdataExplorer", "title": "Launch the shiny application NGSdataExplorer.", "topics": [ "NGSdataExplorer" ] }, { "page": "outlier_filter", "title": "Filter out outliers in metadata, identified by the chosen outlier test.", "concept": [ "Data cleaning and pre-processing" ], "topics": [ "outlier_filter" ] }, { "page": "outliers_by_pool_fragments", "title": "Identify and flag outliers based on pool fragments.", "concept": [ "Data cleaning and pre-processing" ], "topics": [ "outliers_by_pool_fragments" ] }, { "page": "pcr_id_column", "title": "Easily retrieve the name of the pcr id column.", "concept": [ "dynamic vars" ], "topics": [ "pcr_id_column" ] }, { "page": "proto_oncogenes", "title": "Data frames for proto-oncogenes (human and mouse) and tumor-suppressor genes from UniProt.", "topics": [ "proto_oncogenes", "tumor_suppressors" ] }, { "page": "purity_filter", "title": "Filter integration sites based on purity.", "concept": [ "Data cleaning and pre-processing" ], "topics": [ "purity_filter" ] }, { "page": "quantification_types", "title": "Possible choices for the 'quantification_type' parameter.", "concept": [ "Import functions helpers" ], "topics": [ "quantification_types" ] }, { "page": "realign_after_collisions", "title": "Re-aligns matrices of other quantification types based on the processed sequence count matrix.", "concept": [ "Data cleaning and pre-processing" ], "topics": [ "realign_after_collisions" ] }, { "page": "reduced_AF_columns", "title": "Names of the columns of the association file to consider for Vispa2 launch.", "topics": [ "reduced_AF_columns" ] }, { "page": "refGene_table_cols", "title": "Required columns for refGene file.", "topics": [ "refGene_table_cols" ] }, { "page": "refGenes_hg19", "title": "Gene annotation files for hg19, mm9.", "topics": [ "refGenes_hg19", 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"Utilities" ], "topics": [ "separate_quant_matrices" ] }, { "page": "set_mandatory_IS_vars", "title": "Define custom dynamic vars.", "concept": [ "dynamic vars" ], "topics": [ "set_af_columns_def", "set_annotation_IS_vars", "set_iss_stats_specs", "set_mandatory_IS_vars", "vars_setters" ] }, { "page": "set_matrix_file_suffixes", "title": "Sets the look-up table for matrix file suffixes.", "concept": [ "dynamic vars" ], "topics": [ "set_matrix_file_suffixes" ] }, { "page": "sharing_heatmap", "title": "Plot IS sharing heatmaps.", "concept": [ "Plotting functions" ], "topics": [ "sharing_heatmap" ] }, { "page": "sharing_venn", "title": "Produce tables to plot sharing venn or euler diagrams.", "concept": [ "Plotting functions" ], "topics": [ "sharing_venn" ] }, { "page": "top_abund_tableGrob", "title": "Summary top abundant tableGrobs for plots.", "concept": [ "Plotting functions" ], "topics": [ "top_abund_tableGrob" ] }, { "page": "top_cis_overtime_heatmap", "title": "Heatmaps for the top 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