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| edgeR-package | Empirical analysis of digital gene expression data in R |
| alpha.approxeb | Estimate the Prior Weight, Alpha |
| approx.expected.info | Approximate Expected Information (Fisher Information) |
| calcNormFactors | Calculates Normalization Factors for a Matrix of Count Data |
| commonCondLogLikDerDelta | Conditional Log-Likelihoods in Terms of Delta |
| condLogLikDerDelta | Conditional Log-Likelihood in Terms of Delta |
| condLogLikDerSize | Log-Likelihood of the Common Dispersion for a Single Equalized Group |
| de4DGE | Compute Moderated Differential Expression Scores for Digital Gene Expression (DGE) Data |
| de4DGEList-class | differential expression for Digital Gene Expression data - class |
| deDGE | Compute Moderated Differential Expression Scores for Digital Gene Expression (DGE) Data |
| deDGEList-class | differential expression of Digital Gene Expression data - class |
| DGEList | DGEList Constructor |
| DGEList-class | Digital Gene Expression data - class |
| EBList-class | Differential Expression of Digital Gene Expression data - class |
| edgeR | Empirical analysis of digital gene expression data in R |
| equalizeLibSizes | Quantile Adjustment to Equalize Library Sizes for a Fixed Value of the Dispersion Parameter |
| estimateCommonDisp | Estimates the Negative Binomial Common Dispersion by Maximizing the Negative Binomial Conditional Common Likelihood |
| estimateDispIter | Normalizes a Dataset Using Quantile Adjustment and Iteratively Estimates the Dispersion Parameter |
| estimatePs | Estimate Expression Levels |
| estimateSmoothing | Estimate the Prior Weight |
| estimateTagwiseDisp | Maximizes the Negative Binomial Weighted Conditional Likelihood |
| exactTest | An Exact Test for Differences between Two Negative Binomial Groups |
| exactTest.matrix | An Exact Test for Differences between Two Negative Binomial Groups |
| findMaxD2 | Maximizes the Negative Binomial Likelihood |
| getCounts | Extract Table of Counts from DGEList Object |
| interpolateHelper | Quantile Adjustment Interpolator |
| logLikDerP | Log-Likelihood for Proportion |
| maPlot | Plots Log-Fold Change versus Log-Concentration (or, M versus A) for Count Data |
| NC1 | Raw Data for Several SAGE Libraries from the Zhang 1997 Science Paper. |
| NC2 | Raw Data for Several SAGE Libraries from the Zhang 1997 Science Paper. |
| plotFC | Plots log-Fold Change versus log-Concentration (or, M versus A) for Count Data |
| plotSmear | Plots log-Fold Change versus log-Concentration (or, M versus A) for Count Data |
| q2qnbinom | Quantile to Quantile Mapping between Negative-Binomial Distributions |
| q2qpois | Quantile to Quantile Mapping between Negative-Binomial Distributions |
| quantileAdjust | Normalizes a Dataset by Using a Quantile Adjustment |
| readDGE | Read and Merge a Set of Files Containing DGE Data |
| show,de4DGEList-method | differential expression for Digital Gene Expression data - class |
| show,deDGEList-method | differential expression of Digital Gene Expression data - class |
| show,EBList-method | Differential Expression of Digital Gene Expression data - class |
| show,TopTags-method | Table of the Top Differentially Expressed Tags |
| splitIntoGroups | Split the Counts or Pseudocounts from a DGEList Object According To Group |
| splitIntoGroupsPseudo | Split the Counts or Pseudocounts from a DGEList Object According To Group |
| subsetting | Subset DGEList Objects |
| tau2.0.objective | Objective Function for Tau2 |
| topTags | Table of the Top Differentially Expressed Tags |
| TopTags-class | Table of the Top Differentially Expressed Tags |
| Tu102 | Raw Data for Several SAGE Libraries from the Zhang 1997 Science Paper. |
| Tu98 | Raw Data for Several SAGE Libraries from the Zhang 1997 Science Paper. |
| weightedCondLogLikDerDelta | Weighted Conditional Log-Likelihood in Terms of Delta |
| [.DGEList | Subset DGEList Objects |
| [.TopTags | Table of the Top Differentially Expressed Tags |