| .getClassMappedCentrifugeClassificationsSummaries |
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| .getClassMappedSpingoClassificationsSummaries |
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| .getDirectCentrifugeClassificationsSummaries |
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| .getDirectQiimeClassificationsSummaries |
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| .getDirectQiimeProfileSummaries |
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| .getDirectSpingoClassificationsSummaries |
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| .getFamilyMappedCentrifugeClassificationsSummaries |
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| .getFamilyMappedSpingoClassificationsSummaries |
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| .getGenusMappedCentrifugeClassificationsSummaries |
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| .getGenusMappedSpingoClassificationsSummaries |
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| .getMappedQiimeClassificationsSummariesByRank |
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| .getMappedQiimeProfileSummariesByRank |
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| .getOrderMappedCentrifugeClassificationsSummaries |
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| .getOrderMappedSpingoClassificationsSummaries |
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| .getPhylumMappedCentrifugeClassificationsSummaries |
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| .getPhylumMappedSpingoClassificationsSummaries |
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| .getSpeciesMappedCentrifugeClassificationsSummaries |
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| .getSpeciesMappedSpingoClassificationsSummaries |
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| .getSuperkingdomMappedCentrifugeClassificationsSummaries |
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| .getSuperkingdomMappedSpingoClassificationsSummaries |
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| assignCentrifugeProfileAsMetatranscriptomics |
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| assignCentrifugeProfileAsShotgun |
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| assignQiimeProfileAsAmplicons |
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| assignSpingoProfileAsAmplicons |
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| clasifyCentrifugeShotgunSpingoAndQiimeGungaProfile |
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| getPerformanceMeasureForSingleRankAsDataFrame |
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| getStandardIdsDataFrame |
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| getStandardParentIdsAsDataFrame |
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| gungaWorkflowForCentrifugeShotgunSpingoAndQiime |
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| loadQiimeClassifications |
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| loadQiimeProfile |
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| loadRawCentrifugeClassifications |
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| loadRawCentrifugeProfile |
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| loadRawKraken2Classifications |
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| loadRawMajorityVoteProfile |
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| loadRawQiimeOtuTable |
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| loadRawQiimeProfile |
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| loadRawSpingoClassifications |
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| loadRawSpingoProfile |
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| makeCentrifugeProfileForMetatranscriptomics |
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| makeCentrifugeProfileForShotgun |
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| makeQiimeProfileForAmplicon |
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| makeSpingoProfileForAmplicon |
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| mergeProfiles |
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| processCentrifugeClassifications |
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| processCentrifugeProfile |
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| processQiimeProfile |
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| processSpingoClassifications |
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| processSpingoProfile |
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| sayHelloGunga |
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| summarizeCentrifugeClassifications |
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| summarizeQiimeClassifications |
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| summarizeSpingoClassifications |
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|
