API for HIVDiversity/MotifBinner2
Processes NGS Primer ID Datasets
| Global functions | |
|---|---|
| alignBins | Man page Source code |
| alignBinsMSA | Man page Source code |
| alignBinsMSA_internal | Man page Source code |
| alignBinsSP | Man page Source code |
| alignBinsSP_internal | Man page Source code |
| alignBins_internal | Man page Source code |
| alignment_tests | Source code |
| allResults | Man page Source code |
| ambigSeqs | Man page Source code |
| ambigSeqs_internal | Source code |
| applyOperation | Man page Source code |
| apply_consensus_cutoff | Man page Source code |
| basicQC | Man page Source code |
| binSeqErr | Man page Source code |
| binSeqErr_internal | Man page Source code |
| binSizeCheck | Man page Source code |
| blastTrim | Man page Source code |
| buildConfig | Man page Source code |
| buildConfig_nol_test | Man page Source code |
| buildConfig_ol_prod | Man page Source code |
| buildConsensus | Man page Source code |
| buildConsensus_cpp | Source code |
| build_cutoff_models | Man page Source code |
| build_dependency_map | Source code |
| computeMetrics | Man page Source code |
| computeMetrics.alignBins | Source code |
| computeMetrics.alignBinsMSA | Source code |
| computeMetrics.alignBinsSP | Source code |
| computeMetrics.allResults | Source code |
| computeMetrics.ambigSeqs | Source code |
| computeMetrics.basicQC | Source code |
| computeMetrics.binSeqErr | Source code |
| computeMetrics.binSizeCheck | Source code |
| computeMetrics.blastTrim | Source code |
| computeMetrics.buildConsensus | Source code |
| computeMetrics.dataTracing | Source code |
| computeMetrics.doubleClusterTally | Source code |
| computeMetrics.extractData | Source code |
| computeMetrics.extractPIDs | Source code |
| computeMetrics.loadData | Source code |
| computeMetrics.matchPairs | Source code |
| computeMetrics.mergePEAR | Source code |
| computeMetrics.prepConfig | Source code |
| computeMetrics.primerDimer | Source code |
| computeMetrics.primerSeqErr | Source code |
| computeMetrics.processBadPIDs | Source code |
| computeMetrics.qualTrim | Source code |
| computeMetrics.regionSplit | Source code |
| computeMetrics.removeChars | Source code |
| computeMetrics.seqLength | Source code |
| computeMetrics.trimAffixes | Source code |
| computeMetrics.vsearchCluster | Source code |
| dataTracing | Man page Source code |
| doubleClusterTally | Man page Source code |
| dummy_test_debug | Source code |
| excl_inf_max | Source code |
| excl_inf_min | Source code |
| explorePCRAmplificationRates | Source code |
| explorePIDRelationships | Source code |
| extractData | Man page Source code |
| extractPIDs | Man page Source code |
| gapQualityTweaker_non_ol_cpp | Source code |
| gapQualityTweaker_ol_cpp | Source code |
| genKeptVector | Man page Source code |
| genReport | Man page Source code |
| genReport_internal_allResults | Source code |
| genReport_internal_generic | Source code |
| genSummary | Man page Source code |
| genSummary.allResults | Source code |
| genSummary_case1 | Man page Source code |
| genSummary_case3 | Man page Source code |
| genSummary_case4 | Man page Source code |
| genSummary_comb | Source code |
| genSummary_matchPairs | Source code |
| genSummary_one | Source code |
| genSummary_processBadPIDs | Source code |
| getKept | Man page Source code |
| getTrimmed | Man page Source code |
| get_consensus_cutoff | Man page Source code |
| get_cutoff_models | Man page Source code |
| group_cons_bins_internal | Man page Source code |
| kable_summary | Man page Source code |
| loadData | Man page Source code |
| makeIUPACScoreMat | Man page Source code |
| make_monotonic | Man page Source code |
| map_reads_no_ins_cpp | Source code |
| map_reads_with_mafft | Source code |
| matchPairs | Man page Source code |
| memory_optimization | Source code |
| mergePEAR | Man page Source code |
| moving_statistic | Man page Source code |
| mutate_letter | Man page Source code |
| pairWiseMSA_cpp | Source code |
| pairwiseMSA | Man page Source code |
| plot_consensus_cutoff_model | Man page Source code |
| plot_consensus_cutoff_sim | Man page Source code |
| prepConfig | Man page Source code |
| primerDimer | Man page Source code |
| primerSeqErr | Man page Source code |
| print.alignBins | Source code |
| print.alignBinsMSA | Source code |
| print.alignBinsSP | Source code |
| print.allResults | Source code |
| print.ambigSeqs | Source code |
| print.basicQC | Source code |
| print.binSeqErr | Source code |
| print.binSizeCheck | Source code |
| print.blastTrim | Source code |
| print.buildConsensus | Source code |
| print.dataTracing | Source code |
| print.doubleClusterTally | Source code |
| print.extractData | Source code |
| print.extractPIDs | Source code |
| print.loadData | Source code |
| print.matchPairs | Source code |
| print.mergePEAR | Source code |
| print.prepConfig | Source code |
| print.primerDimer | Source code |
| print.primerSeqErr | Source code |
| print.processBadPIDs | Source code |
| print.qualTrim | Source code |
| print.regionSplit | Source code |
| print.removeChars | Source code |
| print.seqLength | Source code |
| print.trimAffixes | Source code |
| print.vsearchCluster | Source code |
| processBadPIDs | Man page Source code |
| processPrimers | Man page Source code |
| purge_all_results | Source code |
| qualTrim | Man page Source code |
| reformat_tallies | Man page Source code |
| regionSplit | Man page Source code |
| regionSplit_cpp | Source code |
| removeChars | Man page Source code |
| removeChars_cpp | Source code |
| saveToDisk | Man page Source code |
| saveToDisk.alignBins | Source code |
| saveToDisk.alignBinsMSA | Source code |
| saveToDisk.alignBinsSP | Source code |
| saveToDisk.allResults | Source code |
| saveToDisk.ambigSeqs | Source code |
| saveToDisk.basicQC | Source code |
| saveToDisk.binSeqErr | Source code |
| saveToDisk.binSizeCheck | Source code |
| saveToDisk.blastTrim | Source code |
| saveToDisk.buildConsensus | Source code |
| saveToDisk.dataTracing | Source code |
| saveToDisk.doubleClusterTally | Source code |
| saveToDisk.extractData | Source code |
| saveToDisk.extractPIDs | Source code |
| saveToDisk.loadData | Source code |
| saveToDisk.matchPairs | Source code |
| saveToDisk.mergePEAR | Source code |
| saveToDisk.prepConfig | Source code |
| saveToDisk.primerDimer | Source code |
| saveToDisk.primerSeqErr | Source code |
| saveToDisk.processBadPIDs | Source code |
| saveToDisk.qualTrim | Source code |
| saveToDisk.regionSplit | Source code |
| saveToDisk.removeChars | Source code |
| saveToDisk.seqLength | Source code |
| saveToDisk.trimAffixes | Source code |
| saveToDisk.vsearchCluster | Source code |
| scoreAlignmentPositions_cpp | Source code |
| seqLength | Man page Source code |
| shortReadQ_forced_append | Man page Source code |
| sim_all_parents_main_off | Man page Source code |
| sim_one_parent_main_off | Man page Source code |
| sim_wrapper | Man page Source code |
| sliceTime | Man page Source code |
| sliceTime_allResults | Source code |
| store_configs | Source code |
| tallyPrimerSeqErrors_cpp | Source code |
| timingTable | Man page Source code |
| timingTable_allResults | Source code |
| timingTable_other | Source code |
| transfer_gaps_cpp | Source code |
| trimAffixes | Man page Source code |
| trimAffixes_internal | Source code |
| trimFront_cpp | Source code |
| vsearchCluster | Man page Source code |
