Man pages for martingarridorc/biokit
Toolkit for the automatic analysis of omics data
| addStatusByCutoff | Add status by cutoff |
| addStatusByRank | Add status by rank |
| autoEdgerComparison | Automatic edgeR analysis from counts |
| autoLimmaComparison | Automatic limma analysis |
| autoPairwiseMatrixTest | Automatic pairwise contrast |
| contrastsFromDesign | Create contrast matrix from design matrix. |
| countsToTmm | Normalize counts with TMM |
| createPairwiseContrasts | Create pariwise contrasts |
| defaultLogFc | Log 2 of means ratio |
| designFromSampInfo | Create design matrix from sample metadata |
| edgerDfFromContrasts | Obtain edgeR results from counts, design and contrasts matrix |
| fisherExactTest | Measure over-representation using Fisher's Exact Test |
| gseaFromStats | Gene set enrichment analysis from statistical results |
| gseaPlot | GSEA plot |
| heatmapPlot | Heatmap plot |
| humanHallmarks | Human MSigDb hallmarks |
| limmaDfFromContrasts | Obtain limma results from data, design and contrasts matrix. |
| messageMappingInfo | Evaluate and print translator df information |
| nsTestPValue | Not sensitive T test p value |
| nsTestT | Non sensitive T Test statistic |
| oraFromStats | Over representation analysis from statistical results |
| overRepresentationAnalysis | Over-representation analysis |
| pairwiseMatrixTest | Generic pairwise matrix test |
| pcaPlot | Simple PCA analysis |
| sarsCovMat | RNA-Seq data of human cell lines infected with sars-cov-2 |
| sarsCovSampInfo | Sample level information for the sars-cov-2 count matrix |
| splitFunMerge | Split, Function and Merge |
| translateMatrix | Translate matrix rownames |
| translateMatrixWithDb | Translate matrix rownames using annotation package |
| validateMatrix | Validate matrix |
| validateSampInfo | Validate sample information |
| validateTranslatorDf | Validate translator data frame |
| violinPlot | Violin plot |
| volcanoPlot | Simple Volcano Plot |
