Package: minSNPs 0.2.0

minSNPs: Resolution-Optimised SNPs Searcher

This is a R implementation of "Minimum SNPs" software as described in "Price E.P., Inman-Bamber, J., Thiruvenkataswamy, V., Huygens, F and Giffard, P.M." (2007) <doi:10.1186/1471-2105-8-278> "Computer-aided identification of polymorphism sets diagnostic for groups of bacterial and viral genetic variants."

Authors:Ludwig Kian Soon Hoon [aut, cre], Peter Shaw [aut, ctb], Phil Giffard [aut, ctb]

minSNPs_0.2.0.tar.gz
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minSNPs.pdf |minSNPs.html✨
minSNPs/json (API)
NEWS

# Install 'minSNPs' in R:
install.packages('minSNPs', repos = c('https://ludwighoon.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/ludwighoon/minsnps/issues

On CRAN:

62 exports 3 stars 1.34 score 10 dependencies 38 scripts 339 downloads

Last updated 6 months agofrom:6c68c77a36. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 16 2024
R-4.5-winOKSep 16 2024
R-4.5-linuxOKSep 16 2024
R-4.4-winOKSep 16 2024
R-4.4-macOKSep 16 2024
R-4.3-winOKSep 16 2024
R-4.3-macOKSep 16 2024

Exports:cal_fncal_fpcal_met_snpcalculate_mcccalculate_mcc_multicalculate_percentcalculate_simpsoncalculate_simpson_by_groupcalculate_variant_within_groupcheck_meta_targetcheck_multistatecheck_percentcombine_fastq_search_resultcombine_search_string_resultcombine_search_string_result_from_filescombine_search_string_result_from_listestimate_coverageextend_lengthfind_optimised_snpsfull_merge_1generate_kmer_search_stringgenerate_kmersgenerate_patterngenerate_prioritisationgenerate_snp_search_stringget_all_process_methodsget_metric_funget_snps_setinfer_from_combinediterate_mergeiterate_throughmap_profile_to_targetmatch_countmcc_calculationmerge_fastaoutput_resultoutput_to_filesparse_group_mccparse_group_mcc_multipredict_balkprocess_alleleprocess_kmer_resultprocess_result_fileprocess_snp_resultprofile_to_group_resultread_fastaread_sequences_from_fastqremove_snp_conflictresolve_IUPAC_missingreverse_complementscramble_sequencesearch_from_fastq_readssearch_from_readssequence_reads_match_countsummarise_resulttrain_balktranslate_positionview_mccview_mcc_multiview_percentview_simpsonwrite_fasta

Dependencies:BHBiocParallelcodetoolscpp11data.tableformatRfutile.loggerfutile.optionslambda.rsnow

MinSNPs Workflow

Rendered fromMinSNPs_Workflow.Rmdusingknitr::rmarkdownon Sep 16 2024.

Last update: 2023-04-19
Started: 2021-08-22

Readme and manuals

Help Manual

Help pageTopics
'binomial_naive_bayes'binomial_naive_bayes
'cal_fn'cal_fn
'cal_fp'cal_fp
'cal_met_snp'cal_met_snp
'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
'identify_group_variant_breakdown'calculate_variant_within_group
'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_kmer_search_string'generate_kmer_search_string
'generate_kmers'generate_kmers
'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_balk'predict_balk
'predict.binomial_naive_bayes'predict.binomial_naive_bayes
'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_conflic'remove_snp_conflict
'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