Man pages for genialis/shRNAde
Functions needed to support the shRNA pipeline in rewolwe-bio
| 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. |
