Files in ludwigHoon/minSNPs
Resolution-Optimised SNPs Searcher
.Rbuildignore
.Rprofile
.devcontainer/devcontainer.json
.github/ISSUE_TEMPLATE/bug_report.md
.github/ISSUE_TEMPLATE/feature_request.md
.gitignore
.lintr
.vscode/settings.json
DESCRIPTION
LICENSE
MinSNPs.Rproj
NAMESPACE
NEWS.md
R/addn_search.R
R/balk.r
R/balk_helper.r
R/guided_helpers.r
R/merge.R
R/output.R
R/process.R
R/search.R
R/search_from_reads.R
R/search_string_generation.R
R/utility.R
R/zzz.R
README.md
WIP/Long_read_Simulation/Experiments.r
WIP/Long_read_Simulation/Experiments_read.r
WIP/Long_read_Simulation/USE_medaka_to_mpileup.R
WIP/Long_read_Simulation/USE_search_string.R
WIP/Long_read_Simulation/USE_typing.R
WIP/Long_read_Simulation/automate_sim2.py
WIP/Long_read_Simulation/balk.r
WIP/Long_read_Simulation/balk_helper.r
WIP/Long_read_Simulation/gene_string.R
WIP/Long_read_Simulation/inference_common.R
WIP/Long_read_Simulation/malaria_mcc_inference.r
WIP/Long_read_Simulation/mcc_custom_metric.r
WIP/Long_read_Simulation/read_2
WIP/Long_read_Simulation/result_collection.R
WIP/Long_read_Simulation/running
WIP/Long_read_Simulation/running2
WIP/Long_read_Simulation/search_string_generation.r
WIP/Long_read_Simulation/simulation_run.R
WIP/Long_read_Simulation/simulation_run.r
WIP/Long_read_Simulation/stats
WIP/Long_read_Simulation/string_generation.R
WIP/Long_read_Simulation/t_sim_result.csv
WIP/Untitled-1.r
WIP/analyse.R
WIP/chlamydia_1.jpg
WIP/chlamydia_2.jpg
WIP/chlamydia_mapped.jpg
WIP/fragments.R
WIP/gen.r
WIP/gen_sim.r
WIP/hd_1.jpg
WIP/hd_2.jpg
WIP/hd_3.jpg
WIP/import.r
WIP/import_success.jpg
WIP/install_rstudio.jpg
WIP/install_success.jpg
WIP/iupac.md
WIP/long_read_hd.R
WIP/parallel.jpg
WIP/percent_1.jpg
WIP/percent_2.jpg
WIP/percent_3.jpg
WIP/process.r
WIP/process_n.R
WIP/pv40-analysis/variant_within_goi.r
WIP/repo_changed.jpg
WIP/saving.jpg
WIP/set_repositories.jpg
WIP/setdirectory.jpg
WIP/setrespository_rstudio.jpg
WIP/sim_long_read.md
WIP/simulation.r
WIP/target_generation.R
WIP/test.R
WIP/usermanual.html
WIP/usermanual.qmd
WIP/usermanual_files/libs/bootstrap/bootstrap-icons.css
WIP/usermanual_files/libs/bootstrap/bootstrap-icons.woff
WIP/usermanual_files/libs/bootstrap/bootstrap.min.css
WIP/usermanual_files/libs/bootstrap/bootstrap.min.js
WIP/usermanual_files/libs/clipboard/clipboard.min.js
WIP/usermanual_files/libs/quarto-html/anchor.min.js
WIP/usermanual_files/libs/quarto-html/popper.min.js
WIP/usermanual_files/libs/quarto-html/quarto-syntax-highlighting.css
WIP/usermanual_files/libs/quarto-html/quarto.js
WIP/usermanual_files/libs/quarto-html/tippy.css
WIP/usermanual_files/libs/quarto-html/tippy.umd.min.js
WIP/window_d_val.R
docs/404.html
docs/LICENSE-text.html
docs/articles/MinSNPs_Workflow.html
docs/articles/index.html
docs/articles/user_manual.html
docs/authors.html
docs/bootstrap-toc.css
docs/bootstrap-toc.js
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/link.svg
docs/news/index.html
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/binomial_naive_bayes.html
docs/reference/branch_and_search.html
docs/reference/cal_fn.html
docs/reference/cal_fp.html
docs/reference/cal_met_snp.html
docs/reference/calculate.percent.html
docs/reference/calculate.simpson.html
docs/reference/calculate_mcc.html
docs/reference/calculate_mcc_multi.html
docs/reference/calculate_percent.html
docs/reference/calculate_simpson.html
docs/reference/calculate_simpson_by_group.html
docs/reference/calculate_state.html
docs/reference/calculate_variant_within_group.html
docs/reference/check_fasta_meta_mapping.html
docs/reference/check_meta_target.html
docs/reference/check_multistate.html
docs/reference/check_percent.html
docs/reference/coef.binomial_naive_bayes.html
docs/reference/combine_fastq_search_result.html
docs/reference/combine_search_string_result.html
docs/reference/combine_search_string_result_from_files.html
docs/reference/combine_search_string_result_from_list.html
docs/reference/estimate_coverage.html
docs/reference/extend_length.html
docs/reference/find_optimised_snps.html
docs/reference/flag_allele.html
docs/reference/flag_position.html
docs/reference/full_merge.html
docs/reference/full_merge_1.html
docs/reference/generate_kmer_search_string.html
docs/reference/generate_kmers.html
docs/reference/generate_pattern.html
docs/reference/generate_prioritisation.html
docs/reference/generate_snp_search_string.html
docs/reference/get_all_process_methods.html
docs/reference/get_binomial_tables.html
docs/reference/get_metric_fun.html
docs/reference/get_positions_to_search.html
docs/reference/get_snps_set.html
docs/reference/get_usual_length.html
docs/reference/identify_overlaps.html
docs/reference/index.html
docs/reference/infer_from_combined.html
docs/reference/iterate_merge.html
docs/reference/iterate_through.html
docs/reference/map_profile_to_target.html
docs/reference/match_count.html
docs/reference/mcc_calculation.html
docs/reference/merge_fasta.html
docs/reference/output_parsed.html
docs/reference/output_result.html
docs/reference/output_to_files.html
docs/reference/parse_group_mcc.html
docs/reference/parse_group_mcc_multi.html
docs/reference/predict.binomial_naive_bayes.html
docs/reference/predict_balk.html
docs/reference/print.binomial_naive_bayes.html
docs/reference/process_allele.html
docs/reference/process_kmer_result.html
docs/reference/process_result_file.html
docs/reference/process_snp_result.html
docs/reference/profile_to_group_result.html
docs/reference/read.fasta.html
docs/reference/read_fasta.html
docs/reference/read_sequences_from_fastq.html
docs/reference/remove_dup_allele.html
docs/reference/remove_dup_isolate.html
docs/reference/remove_snp_conflict.html
docs/reference/resolve_IUPAC_missing.html
docs/reference/reverse_complement.html
docs/reference/scramble_sequence.html
docs/reference/search_from_fastq_reads.html
docs/reference/search_from_reads.html
docs/reference/select_n_set_i_depth.html
docs/reference/sequence_reads_match_count.html
docs/reference/summarise_result.html
docs/reference/summary.binomial_naive_bayes.html
docs/reference/train_balk.html
docs/reference/transform_snp.html
docs/reference/translate_position.html
docs/reference/usual_length.html
docs/reference/view_mcc.html
docs/reference/view_mcc_multi.html
docs/reference/view_percent.html
docs/reference/view_simpson.html
docs/reference/write_fasta.html
docs/sitemap.xml
docs/usermanual.pdf
inst/extdata/Chlamydia_1.fasta
inst/extdata/Chlamydia_2.fasta
inst/extdata/Chlamydia_mapped.fasta
man/binomial_naive_bayes.Rd
man/branch_and_search.Rd
man/cal_fn.Rd
man/cal_fp.Rd
man/cal_met_snp.Rd
man/calculate_mcc.Rd
man/calculate_mcc_multi.Rd
man/calculate_percent.Rd
man/calculate_simpson.Rd
man/calculate_simpson_by_group.Rd
man/calculate_state.Rd
man/calculate_variant_within_group.Rd
man/check_fasta_meta_mapping.Rd
man/check_meta_target.Rd
man/check_multistate.Rd
man/check_percent.Rd
man/coef.binomial_naive_bayes.Rd
man/combine_fastq_search_result.Rd
man/combine_search_string_result.Rd
man/combine_search_string_result_from_files.Rd
man/combine_search_string_result_from_list.Rd
man/estimate_coverage.Rd
man/extend_length.Rd
man/find_optimised_snps.Rd
man/flag_allele.Rd
man/flag_position.Rd
man/full_merge.Rd
man/full_merge_1.Rd
man/generate_kmer_search_string.Rd
man/generate_kmers.Rd
man/generate_pattern.Rd
man/generate_prioritisation.Rd
man/generate_snp_search_string.Rd
man/get_all_process_methods.Rd
man/get_binomial_tables.Rd
man/get_metric_fun.Rd
man/get_positions_to_search.Rd
man/get_snps_set.Rd
man/get_usual_length.Rd
man/identify_overlaps.Rd
man/infer_from_combined.Rd
man/iterate_merge.Rd
man/iterate_through.Rd
man/map_profile_to_target.Rd
man/match_count.Rd
man/mcc_calculation.Rd
man/merge_fasta.Rd
man/output_parsed.Rd
man/output_result.Rd
man/output_to_files.Rd
man/parse_group_mcc.Rd
man/parse_group_mcc_multi.Rd
man/predict.binomial_naive_bayes.Rd
man/predict_balk.Rd
man/print.binomial_naive_bayes.Rd
man/process_allele.Rd
man/process_kmer_result.Rd
man/process_result_file.Rd
man/process_snp_result.Rd
man/profile_to_group_result.Rd
man/read_fasta.Rd
man/read_sequences_from_fastq.Rd
man/remove_dup_isolate.Rd
man/remove_snp_conflict.Rd
man/resolve_IUPAC_missing.Rd
man/reverse_complement.Rd
man/scramble_sequence.Rd
man/search_from_fastq_reads.Rd
man/search_from_reads.Rd
man/select_n_set_i_depth.Rd
man/sequence_reads_match_count.Rd
man/summarise_result.Rd
man/summary.binomial_naive_bayes.Rd
man/train_balk.Rd
man/transform_snp.Rd
man/translate_position.Rd
man/view_mcc.Rd
man/view_mcc_multi.Rd
man/view_percent.Rd
man/view_simpson.Rd
man/write_fasta.Rd
minSNPs_app/app.R
minSNPs_app/private_dependency.R
minSNPs_app/rsconnect/shinyapps.io/ldwgksh/minsnps_app.dcf
minSNPs_app/server.R
minSNPs_app/ui.R
minsnps_standard_workflow.R
pkgdown/_pkgdown.yml
pkgdown/assets/usermanual.pdf
tests/testthat.R
tests/testthat/test-process.R
tests/testthat/test-search.R
vignettes/.build.timestamp
vignettes/.gitignore
vignettes/MinSNPs_Workflow.Rmd
