Files in calabrialab/ISAnalytics

Analyze gene therapy vector insertion sites data identified from genomics next generation sequencing reads for clonal tracking studies

LICENSE.md NEWS.Rmd NEWS.md R/ISAnalytics-deprecated.R R/ISAnalytics-package.R R/aggregate-functions.R R/analysis-functions.R R/collision-removal.R R/data.R R/exported-vars.R R/import-functions.R R/internal-classes.R R/internal-functions.R R/internal-msgs.R R/outlier-filtering.R R/plotting-functions.R R/population-size-estimate.R R/purity-filter.R R/recalibration-functions.R R/report-utilities.R R/server.R R/ui.R R/utility-functions.R R/zzz.R README.Rmd README.md index.md inst/rmd/af-fs-alignment.Rmd inst/rmd/af-report.Rmd inst/rmd/collision-report.Rmd inst/rmd/install_and_options.Rmd inst/rmd/iss-import-report.Rmd inst/rmd/iss_stats_fragment.Rmd inst/rmd/matrix-import-report.Rmd inst/rmd/outlier-filter-report.Rmd inst/rmd/outlier-report.Rmd inst/script/data.R man-roxygen/genes_db.R man-roxygen/report_path_param.R man-roxygen/transform_list.R man-roxygen/vars_lookuptable_str.R man/CIS_grubbs.Rd man/CIS_grubbs_overtime.Rd man/CIS_volcano_plot.Rd man/HSC_population_plot.Rd man/HSC_population_size_estimate.Rd man/ISAnalytics-deprecated.Rd man/ISAnalytics.Rd man/NGSdataExplorer.Rd man/aggregate_metadata.Rd man/aggregate_values_by_key.Rd man/annotation_issues.Rd man/as_sparse_matrix.Rd man/association_file.Rd man/available_outlier_tests.Rd man/available_tags.Rd man/blood_lineages_default.Rd man/circos_genomic_density.Rd man/clinical_relevant_suspicious_genes.Rd man/comparison_matrix.Rd man/compute_abundance.Rd man/compute_near_integrations.Rd man/cumulative_count_union.Rd man/cumulative_is.Rd man/date_formats.Rd man/default_af_transform.Rd man/default_iss_file_prefixes.Rd man/default_meta_agg.Rd man/default_rec_agg_lambdas.Rd man/default_report_path.Rd man/default_stats.Rd man/enable_progress_bars.Rd man/export_ISA_settings.Rd man/fisher_scatterplot.Rd man/gene_frequency_fisher.Rd man/generate_Vispa2_launch_AF.Rd man/generate_blank_association_file.Rd man/generate_default_folder_structure.Rd man/import_ISA_settings.Rd man/import_Vispa2_stats.Rd man/import_association_file.Rd man/import_parallel_Vispa2Matrices.Rd man/import_parallel_Vispa2Matrices_auto.Rd man/import_parallel_Vispa2Matrices_interactive.Rd man/import_single_Vispa2Matrix.Rd man/inspect_tags.Rd man/integration_alluvial_plot.Rd man/integration_matrices.Rd man/is_sharing.Rd man/iss_source.Rd man/known_clinical_oncogenes.Rd man/mandatory_IS_vars.Rd man/matching_options.Rd man/outlier_filter.Rd man/outliers_by_pool_fragments.Rd man/pcr_id_column.Rd man/proto_oncogenes.Rd man/purity_filter.Rd man/quantification_types.Rd man/realign_after_collisions.Rd man/reduced_AF_columns.Rd man/refGene_table_cols.Rd man/refGenes_hg19.Rd man/remove_collisions.Rd man/reset_mandatory_IS_vars.Rd man/sample_statistics.Rd man/separate_quant_matrices.Rd man/set_mandatory_IS_vars.Rd man/set_matrix_file_suffixes.Rd man/sharing_heatmap.Rd man/sharing_venn.Rd man/threshold_filter.Rd man/top_abund_tableGrob.Rd man/top_cis_overtime_heatmap.Rd man/top_integrations.Rd man/top_targeted_genes.Rd man/transform_columns.Rd man/unzip_file_system.Rd tests/testthat.R tests/testthat/setup.R tests/testthat/test-abundance.R tests/testthat/test-aggregate-functions.R tests/testthat/test-analysis-functions.R tests/testthat/test-cis-grubbs.R tests/testthat/test-collision-removal.R tests/testthat/test-dynamic-vars.R tests/testthat/test-import-af.R tests/testthat/test-import-im-par.R tests/testthat/test-import-im-single.R tests/testthat/test-import-vispa-stats.R tests/testthat/test-is-sharing.R tests/testthat/test-population-size-estimate.R tests/testthat/test-purity-filter.R tests/testthat/test-raw-reads-filtering.R tests/testthat/test-recalibration-functions.R tests/testthat/test-utility-functions.R vignettes/ISAnalytics.Rmd vignettes/workflow_start.Rmd