ISAnalytics-package	ISAnalytics
aggregate_metadata	aggregate_metadata
aggregate_values_by_key	aggregate_values_by_key
annotation_issues	annotation_issues
annotation_IS_vars	mandatory_IS_vars
association_file	association_file
association_file_columns	mandatory_IS_vars
as_sparse_matrix	as_sparse_matrix
available_outlier_tests	available_outlier_tests
available_tags	available_tags
blood_lineages_default	blood_lineages_default
circos_genomic_density	circos_genomic_density
CIS_grubbs	CIS_grubbs
CIS_grubbs_overtime	CIS_grubbs_overtime
CIS_volcano_plot	CIS_volcano_plot
clinical_relevant_suspicious_genes	clinical_relevant_suspicious_genes
comparison_matrix	comparison_matrix
compute_abundance	compute_abundance
compute_near_integrations	compute_near_integrations
cumulative_count_union	cumulative_count_union
cumulative_is	cumulative_is
date_formats	date_formats
default_af_transform	default_af_transform
default_iss_file_prefixes	default_iss_file_prefixes
default_meta_agg	default_meta_agg
default_rec_agg_lambdas	default_rec_agg_lambdas
default_report_path	default_report_path
default_stats	default_stats
enable_progress_bars	enable_progress_bars
export_ISA_settings	export_ISA_settings
fisher_scatterplot	fisher_scatterplot
generate_blank_association_file	generate_blank_association_file
generate_default_folder_structure	generate_default_folder_structure
generate_Vispa2_launch_AF	generate_Vispa2_launch_AF
gene_frequency_fisher	gene_frequency_fisher
HSC_population_plot	HSC_population_plot
HSC_population_size_estimate	HSC_population_size_estimate
import_association_file	import_association_file
import_ISA_settings	import_ISA_settings
import_parallel_Vispa2Matrices	import_parallel_Vispa2Matrices
import_parallel_Vispa2Matrices_auto	import_parallel_Vispa2Matrices_auto
import_parallel_Vispa2Matrices_interactive	import_parallel_Vispa2Matrices_interactive
import_single_Vispa2Matrix	import_single_Vispa2Matrix
import_Vispa2_stats	import_Vispa2_stats
inspect_tags	inspect_tags
integration_alluvial_plot	integration_alluvial_plot
integration_matrices	integration_matrices
ISAnalytics	ISAnalytics
ISAnalytics-deprecated	ISAnalytics-deprecated
iss_source	iss_source
iss_stats_specs	mandatory_IS_vars
is_sharing	is_sharing
known_clinical_oncogenes	known_clinical_oncogenes
mandatory_IS_vars	mandatory_IS_vars
matching_options	matching_options
matrix_file_suffixes	mandatory_IS_vars
NGSdataExplorer	NGSdataExplorer
outliers_by_pool_fragments	outliers_by_pool_fragments
outlier_filter	outlier_filter
pcr_id_column	pcr_id_column
proto_oncogenes	proto_oncogenes
purity_filter	purity_filter
quantification_types	quantification_types
realign_after_collisions	realign_after_collisions
reduced_AF_columns	reduced_AF_columns
refGenes_hg19	refGenes_hg19
refGenes_mm9	refGenes_hg19
refGene_table_cols	refGene_table_cols
remove_collisions	remove_collisions
reset_af_columns_def	reset_mandatory_IS_vars
reset_annotation_IS_vars	reset_mandatory_IS_vars
reset_dyn_vars_config	reset_mandatory_IS_vars
reset_iss_stats_specs	reset_mandatory_IS_vars
reset_mandatory_IS_vars	reset_mandatory_IS_vars
reset_matrix_file_suffixes	reset_mandatory_IS_vars
sample_statistics	sample_statistics
separate_quant_matrices	separate_quant_matrices
set_af_columns_def	set_mandatory_IS_vars
set_annotation_IS_vars	set_mandatory_IS_vars
set_iss_stats_specs	set_mandatory_IS_vars
set_mandatory_IS_vars	set_mandatory_IS_vars
set_matrix_file_suffixes	set_matrix_file_suffixes
sharing_heatmap	sharing_heatmap
sharing_venn	sharing_venn
threshold_filter	threshold_filter
top_abund_tableGrob	top_abund_tableGrob
top_cis_overtime_heatmap	top_cis_overtime_heatmap
top_integrations	top_integrations
top_targeted_genes	top_targeted_genes
transform_columns	transform_columns
tumor_suppressors	proto_oncogenes
unzip_file_system	unzip_file_system
vars_getters	mandatory_IS_vars
vars_resetters	reset_mandatory_IS_vars
vars_setters	set_mandatory_IS_vars
