binomial_naive_bayes |
'binomial_naive_bayes' |
calculate_mcc |
'calculate_mcc' |
calculate_mcc_multi |
'calculate_mcc_multi' |
calculate_percent |
'calculate_percent' |
calculate_simpson |
'calculate_simpson' |
calculate_simpson_by_group |
'calculate_simpson_by_group' |
calculate_state |
'calculate_state' |
calculate_variant_within_group |
'identify_group_variant_breakdown' |
cal_fn |
'cal_fn' |
cal_fp |
'cal_fp' |
cal_met_snp |
'cal_met_snp' |
check_fasta_meta_mapping |
'check_fasta_meta_mapping' |
check_meta_target |
'check_meta_target' |
check_multistate |
'check_multistate' |
check_percent |
'check_percent' |
coef.binomial_naive_bayes |
'coef.binomial_naive_bayes' |
combine_fastq_search_result |
'combine_fastq_search_result' |
combine_search_string_result |
'combine_search_string_result' |
combine_search_string_result_from_files |
'combine_search_string_result_from_files' |
combine_search_string_result_from_list |
'combine_search_string_result_from_list' |
estimate_coverage |
'estimate_coverage' |
extend_length |
'extend_length' |
find_optimised_snps |
'find_optimised_snps' |
full_merge |
'full_merge' |
full_merge_1 |
'full_merge_1' |
generate_kmers |
'generate_kmers' |
generate_kmer_search_string |
'generate_kmer_search_string' |
generate_pattern |
'generate_pattern' |
generate_prioritisation |
'generate_prioritisation' |
generate_snp_search_string |
'generate_snp_search_string' |
get_all_process_methods |
'get_all_process_methods' |
get_binomial_tables |
'get_binomial_tables' |
get_metric_fun |
'get_metric_fun' |
get_snps_set |
'get_snps_set' |
identify_overlaps |
'identify_overlaps' |
infer_from_combined |
'infer_from_combined' |
iterate_merge |
'iterate_merge' |
iterate_through |
'iterate_through' |
map_profile_to_target |
'map_profile_to_target' |
match_count |
'match_count' |
mcc_calculation |
'mcc_calculation' |
merge_fasta |
'merge_fasta' |
output_result |
'output_result' |
output_to_files |
'output_to_files' |
parse_group_mcc |
'parse_group_mcc' |
parse_group_mcc_multi |
'parse_group_mcc_multi' |
predict.binomial_naive_bayes |
'predict.binomial_naive_bayes' |
predict_balk |
'predict_balk' |
print.binomial_naive_bayes |
'print.binomial_naive_bayes' |
process_allele |
'process_allele' |
process_kmer_result |
'process_kmer_result' |
process_result_file |
'process_result_file' |
process_snp_result |
'process_snp_result' |
profile_to_group_result |
'profile_to_group_result' |
read_fasta |
'read_fasta' |
read_sequences_from_fastq |
'read_sequences_from_fastq' |
remove_snp_conflict |
'remove_snp_conflic' |
resolve_IUPAC_missing |
'resolve_IUPAC_missing' |
reverse_complement |
'reverse_complement' |
scramble_sequence |
'scramble_sequence' |
search_from_fastq_reads |
'search_from_fastq_reads' |
search_from_reads |
'search_from_reads' |
sequence_reads_match_count |
'sequence_reads_match_count' |
summarise_result |
'summarise_result' |
summary.binomial_naive_bayes |
'summary.binomial_naive_bayes' |
train_balk |
'train_balk' |
transform_snp |
'transform_snp' |
translate_position |
'translate_position' |
view_mcc |
'view_mcc' |
view_mcc_multi |
'view_mcc_multi' |
view_percent |
'view_percent' |
view_simpson |
'view_simpson' |
write_fasta |
'write_fasta' |