Files in ISAnalytics

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

NEWS.md README.md R/analysis-functions.R R/ISAnalytics-package.R R/internal-msgs.R R/internal-functions.R R/collision-removal.R R/plotting-functions.R R/utility-functions.R R/exported-vars.R R/aggregate-functions.R R/zzz.R R/internal-widgets.R R/import-functions.R R/recalibration-functions.R inst/doc/how_to_import_functions.Rmd inst/doc/aggregate_function_usage.Rmd inst/doc/how_to_import_functions.R inst/doc/collision_removal.R inst/doc/collision_removal.Rmd inst/doc/no_rstudio_usage.R inst/doc/aggregate_function_usage.R inst/doc/no_rstudio_usage.Rmd inst/script/data.R build/ISAnalytics.pdf tests/testthat.R tests/testthat/test-import-im-single.R tests/testthat/test-top-integrations.R tests/testthat/test-utility-functions.R tests/testthat/test-import-af.R tests/testthat/test-abundance.R tests/testthat/test-aggregate-functions.R tests/testthat/test-import-im-par.R tests/testthat/test-collision-removal.R tests/testthat/test-recalibration-functions.R tests/testthat/test-internal-general-purpose-functions.R tests/testthat/test-analysis-functions.R vignettes/how_to_import_functions.Rmd vignettes/aggregate_function_usage.Rmd vignettes/collision_removal.Rmd vignettes/no_rstudio_usage.Rmd man/import_parallel_Vispa2Matrices_auto.Rd man/unzip_file_system.Rd man/aggregate_values_by_key.Rd man/sample_statistics.Rd man/mandatory_IS_vars.Rd man/comparison_matrix.Rd man/as_sparse_matrix.Rd man/date_columns_coll.Rd man/annotation_IS_vars.Rd man/compute_near_integrations.Rd man/ISAnalytics.Rd man/cumulative_count_union.Rd man/quantification_types.Rd man/matching_options.Rd man/import_association_file.Rd man/aggregate_metadata.Rd man/top_integrations.Rd man/realign_after_collisions.Rd man/CIS_volcano_plot.Rd man/remove_collisions.Rd man/default_stats.Rd man/reduced_AF_columns.Rd man/known_clinical_oncogenes.Rd man/association_file_columns.Rd man/threshold_filter.Rd man/separate_quant_matrices.Rd man/import_parallel_Vispa2Matrices_interactive.Rd man/import_single_Vispa2Matrix.Rd man/generate_Vispa2_launch_AF.Rd man/clinical_relevant_suspicious_genes.Rd man/date_formats.Rd man/generate_blank_association_file.Rd man/compute_abundance.Rd man/CIS_grubbs.Rd