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

Package index
Search the calabrialab/ISAnalytics package
Vignettes
Functions
378
Source code
44
Man pages
77
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calabrialab/ISAnalytics: Analyze gene therapy vector insertion sites data identified from genomics next generation sequencing reads for clonal tracking studies
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API

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

Global functions
.additional_ad_samples_msg Source code
.af_col_types Source code
.af_empty_msg Source code
.af_missing_path_error Source code
.af_missing_pathfolder_error Source code
.af_not_aligned_err Source code
.af_not_imported_err Source code
.agg_iss_cols Source code
.agg_key_not_found_err Source code
.agg_with_null_meta_err Source code
.aggregate_lambda Source code
.aggregate_meta Source code
.all_match Source code
.alluvial_plot Source code
.annotation_IS_types Source code
.any_match Source code
.apply_col_transform Source code
.apply_flag_logic Source code
.assign_iss_by_tp Source code
.base_param_check Source code
.check_af_correctness Source code
.check_col_correct Source code
.check_cols_to_compare_param Source code
.check_comparators_param Source code
.check_file_extension Source code
.check_file_system_alignment Source code
.check_length_list_params Source code
.check_length_vector_params Source code
.check_mandatory_vars Source code
.check_parallel_packages Source code
.check_required_cols Source code
.check_same_info Source code
.check_sample_col Source code
.check_stats Source code
.check_threshold_param Source code
.cis_grubb_calc Source code
.cis_join_ref Source code
.cis_param_check Source code
.clean_data Source code
.clean_file_path Source code
.closed_m0_est Source code
.closed_mthchaobc_est Source code
.collisions_check_input_af Source code
.collisions_check_input_matrices Source code
.collisions_obtain_report_summaries Source code
.collisions_obtain_sharing_heatmaps Source code
.comparators_err Source code
.compressed_formats Source code
.consecutive_m0bc_est Source code
.consecutive_mth_est Source code
.convert_dates Source code
.convert_to_captures_matrix Source code
.count_distinct_is_per_gene Source code
.count_group_union Source code
.default_af_cols Source code
.default_annotation_IS_vars Source code
.default_iss_stats_specs Source code
.default_mandatory_IS_vars Source code
.diff_leng_args Source code
.discriminate_by_date Source code
.discriminate_by_replicate Source code
.discriminate_by_seqCount Source code
.estimate_pop Source code
.eval_tag_duplicates Source code
.eval_tag_types Source code
.execute_map_job Source code
.expand_cis_df Source code
.filter_db Source code
.find_exp_cols Source code
.find_in_common Source code
.find_unique_max Source code
.flag_cond_outliers_pool_frag Source code
.four_step_check Source code
.generate_correct Source code
.generate_incorrect Source code
.generate_report_filename Source code
.generate_suffix_specs Source code
.get_def_workers Source code
.get_default_rep_filename Source code
.get_sugg_packages Source code
.get_template Source code
.identify_independent_samples Source code
.import_single_matrix Source code
.import_stats_iss Source code
.import_type Source code
.inform_skip_count_is Source code
.is_annotated Source code
.key_without_tp_err Source code
.keys_not_char_err Source code
.lentiviral_CIS_paper Source code
.list_names_to_mod Source code
.list_params_err Source code
.load_onco_ts_genes Source code
.lookup_matrices Source code
.lookup_matrices_auto Source code
.manage_anomalies_auto Source code
.manage_association_file Source code
.mandatory_IS_types Source code
.match_celltypes_tissues Source code
.matrix_annotated_suffixes Source code
.matrix_not_annotated_suffixes Source code
.melt_datatable Source code
.melt_in_parallel Source code
.melt_tidyr Source code
.merge_onco_tumsup Source code
.meta_not_agg_err Source code
.missing_af_needed_cols Source code
.missing_af_samples_msg Source code
.missing_cAmp_sub_msg Source code
.missing_complAmpID_error Source code
.missing_mand_vars Source code
.missing_needed_cols Source code
.missing_num_cols_error Source code
.missing_pkg_error Source code
.missing_req_cols Source code
.missing_user_cols_error Source code
.missing_user_cols_list_error Source code
.missing_user_cols_meta_error Source code
.modal_warning_data Source code
.na_in_date_col Source code
.names_list_param_err Source code
.nas_introduced_msg Source code
.new_IS_vars_checks Source code
.no_collisions_msg Source code
.no_data_supp Source code
.no_stat_files_imported Source code
.no_stats_import_err Source code
.non_ISM_error Source code
.non_df_input_err Source code
.non_function_elem_error Source code
.non_num_user_cols_error Source code
.non_quant_cols_error Source code
.non_quant_cols_msg Source code
.non_standard_annotation_structure Source code
.not_min_key_err Source code
.onAttach Source code
.only_zero_tp Source code
.outlier_pool_frag_base_checks Source code
.outlier_test_verify_logiop Source code
.parallel_import_merge Source code
.param_names_not_equal_err Source code
.param_names_not_in_list_err Source code
.path_cols_names Source code
.pattern_matching Source code
.per_pool_stats Source code
.pool_frag_calc Source code
.pre_manage_af Source code
.process_af_for_gen Source code
.process_collisions Source code
.process_iss_for_gen Source code
.process_m_for_gen Source code
.process_pool_frag Source code
.produce_report Source code
.quantifications_names_err Source code
.re_agg_and_estimate Source code
.re_agg_and_filter Source code
.read_af Source code
.read_with_fread Source code
.read_with_readr Source code
.report_fail_err Source code
.report_saved_info Source code
.seqCount_col_err Source code
.seqCount_df_err Source code
.sh_obtain_lookup Source code
.sh_row_permut Source code
.sh_truth_tbl_venn Source code
.sharing_for_source Source code
.sharing_multdf_mult_key Source code
.sharing_multdf_single_key Source code
.sharing_singledf_mult_key Source code
.sharing_singledf_single_key Source code
.single_row_sharing Source code
.sliding_window Source code
.split_df_in_chunks Source code
.stats_report Source code
.summary_af_import_msg Source code
.summary_input Source code
.summary_ism_import_msg Source code
.summary_table Source code
.supported_fread_compression_formats Source code
.templates_folder Source code
.templates_info Source code
.tests_pool_frag Source code
.tf_data_frame Source code
.tf_list Source code
.threshold_err Source code
.timepoint_to_months Source code
.timepoint_to_years Source code
.trace_anomalies Source code
.types_mapping Source code
.unnamed_keys_warn Source code
.unnamed_list_err Source code
.unsupported_comp_format_inf Source code
.update_af_after_alignment Source code
.update_as_option Source code
.update_rec_map Source code
.validate_outlier_output_format Source code
.vispa2_paper_link Source code
.vispa2_paper_title Source code
.xls_file_warning Source code
CIS_grubbs Man page Source code
CIS_grubbs_overtime Man page Source code
CIS_volcano_plot Man page Source code
HSC_population_plot Man page Source code
HSC_population_size_estimate Man page Source code
ISAnalytics Man page
ISAnalytics-deprecated Man page
NGSdataExplorer Man page Source code
aggregate_metadata Man page Source code
aggregate_values_by_key Man page Source code
annotation_IS_vars Man page Source code
annotation_issues Man page Source code
as_sparse_matrix Man page Source code
association_file Man page
association_file_columns Man page Source code
available_outlier_tests Man page Source code
available_tags Man page Source code
blood_lineages_default Man page Source code
circos_genomic_density Man page Source code
clinical_relevant_suspicious_genes Man page Source code
comparison_matrix Man page Source code
compute_abundance Man page Source code
compute_near_integrations Man page Source code
cumulative_count_union Man page Source code
cumulative_is Man page Source code
date_formats Man page Source code
default_af_transform Man page Source code
default_iss_file_prefixes Man page Source code
default_meta_agg Man page Source code
default_rec_agg_lambdas Man page Source code
default_report_path Man page Source code
default_stats Man page Source code
enable_progress_bars Man page Source code
export_ISA_settings Man page Source code
fisher_scatterplot Man page Source code
flag_logics Source code
gene_frequency_fisher Man page Source code
generate_Vispa2_launch_AF Man page Source code
generate_blank_association_file Man page Source code
generate_default_folder_structure Man page Source code
import_ISA_settings Man page Source code
import_Vispa2_stats Man page Source code
import_association_file Man page Source code
import_parallel_Vispa2Matrices Man page Source code
import_parallel_Vispa2Matrices_auto Man page Source code
import_parallel_Vispa2Matrices_interactive Man page Source code
import_single_Vispa2Matrix Man page Source code
inspect_tags Man page Source code
integration_alluvial_plot Man page Source code
integration_matrices Man page
is_sharing Man page Source code
iss_source Man page Source code
iss_stats_specs Man page Source code
known_clinical_oncogenes Man page Source code
mandatory_IS_vars Man page Source code
matching_options Man page Source code
matrix_file_suffixes Man page Source code
outlier_filter Man page Source code
outliers_by_pool_fragments Man page Source code
pcr_id_column Man page Source code
proto_oncogenes Man page
purity_filter Man page Source code
quantification_types Man page Source code
realign_after_collisions Man page Source code
reduced_AF_columns Man page Source code
refGene_table_cols Man page Source code
refGenes_hg19 Man page
refGenes_mm9 Man page
remove_collisions Man page Source code
reset_af_columns_def Man page Source code
reset_annotation_IS_vars Man page Source code
reset_dyn_vars_config Man page Source code
reset_iss_stats_specs Man page Source code
reset_mandatory_IS_vars Man page Source code
reset_matrix_file_suffixes Man page Source code
sample_statistics Man page Source code
separate_quant_matrices Man page Source code
set_af_columns_def Man page Source code
set_annotation_IS_vars Man page Source code
set_iss_stats_specs Man page Source code
set_mandatory_IS_vars Man page Source code
set_matrix_file_suffixes Man page Source code
sharing_heatmap Man page Source code
sharing_venn Man page Source code
threshold_filter Man page Source code
top_abund_tableGrob Man page Source code
top_cis_overtime_heatmap Man page Source code
top_integrations Man page Source code
top_targeted_genes Man page Source code
transform_columns Man page Source code
tumor_suppressors Man page
unzip_file_system Man page Source code
vars_getters Man page
vars_resetters Man page
vars_setters Man page
calabrialab/ISAnalytics documentation built on Nov. 2, 2023, 8:57 p.m.

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