classifyDE | Classify DE result |
countClassified | Count classified results |
differentialExpression | Perform differential expression based on specified design |
doDE | Make differential expression analysis |
fetchGeneOrHairpin | Process string to extract shRNA or gene |
fetchTHvalue | Return specified threshold value. |
importClassificationParams | Import parameters used for classification |
importContrastList | Import contrast list |
importExpressionsData | Import expression data based on sample key. |
importOverallContrasts | Import overall contrasts |
importSampleKey | Import sample key |
makeLibrary | Create library of shRNA |
scrapeDEresults | Scrape DESeq2 results and format in reusable format |
summaryTable | Summary and count table of shRNA by sample |
trimResults | Trim results of NAs. |
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