Reading & processing input for further analysis | Identifying SNPs with high Simpson's index | Identifying SNPs discriminating a group of interest | Displaying/saving result
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:
minSNPs_0.2.0.tar.gz
minSNPs_0.2.0.zip(r-4.7-any)minSNPs_0.2.0.zip(r-4.6-any)minSNPs_0.2.0.zip(r-4.5-any)
minSNPs_0.2.0.tgz(r-4.6-any)minSNPs_0.2.0.tgz(r-4.5-any)
minSNPs_0.2.0.tar.gz(r-4.7-any)minSNPs_0.2.0.tar.gz(r-4.6-any)
minSNPs_0.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
minSNPs/json (API)
| # Install 'minSNPs' in R: |
| install.packages('minSNPs', repos = c('https://ludwighoon.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/ludwighoon/minsnps/issues
Last updated from:6c68c77a36. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 200 | ||
| source / vignettes | OK | 258 | ||
| linux-release | OK | 153 | ||
| macos-release | OK | 192 | ||
| macos-oldrel | OK | 207 | ||
| windows-devel | OK | 94 | ||
| windows-release | OK | 108 | ||
| windows-oldrel | OK | 92 | ||
| wasm-release | OK | 115 |
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
