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| alpha.approxeb | Estimate the prior weight, alpha |
| approx.expected.info | Approximate of expected information (Fisher information) |
| condLogLikDerDelta | Conditional log-likelihood in terms of delta |
| condLogLikDerSize | Conditional log-likelihood in terms of size |
| deDGE | Compute moderated differential expression scores for digital gene expression (DGE) data |
| deDGEList-class | differential expression of Digital Gene Expression data - class |
| DGEList | Digital Gene Expression data - class |
| DGEList-class | Digital Gene Expression data - class |
| EBList-class | differential expression of Digital Gene Expression data - class |
| estimatePs | Estimate expression proportions |
| exactTestNB | An exact test for differences between two negative binomial groups |
| findMaxD2 | Maximizes the negative binomial likelihood |
| getData | Extract data table from DGEList object |
| interpolateHelper | Quantile Adjustment interpolator |
| logLikDerP | Log-likelihood for proportion |
| 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. |
| plotMA | MA-like plot for deDGEList objects |
| quantileAdjust | Normalizes a dataset by using a quantile adjustment |
| readDGE | Read a list of files containing DGE data |
| show,deDGEList-method | differential expression of Digital Gene Expression data - class |
| show,DGEList-method | Digital Gene Expression data - class |
| show,EBList-method | differential expression of Digital Gene Expression data - class |
| splitIntoGroups | Split the data from a DGEList object according to group |
| splitIntoGroupsPseudo | Split pseudodata according to group |
| tau2.0.objective | Objective function for tau2 |
| topTags | Displays the top differentially expressed tags in a table |
| 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. |