Differential gene expression analysis based on the negative binomial distribution

coef | Extract a matrix of model coefficients/standard errors |

collapseReplicates | Collapse technical replicates in a RangedSummarizedExperiment... |

counts | Accessors for the 'counts' slot of a DESeqDataSet object. |

DESeq | Differential expression analysis based on the Negative... |

DESeq2-package | DESeq2 package for differential analysis of count data |

DESeqDataSet | DESeqDataSet object and constructors |

DESeqResults | DESeqResults object and constructor |

DESeqTransform | DESeqTransform object and constructor |

design | Accessors for the 'design' slot of a DESeqDataSet object. |

dispersionFunction | Accessors for the 'dispersionFunction' slot of a DESeqDataSet... |

dispersions | Accessor functions for the dispersion estimates in a... |

estimateBetaPriorVar | Steps for estimating the beta prior variance |

estimateDispersions | Estimate the dispersions for a DESeqDataSet |

estimateDispersionsGeneEst | Low-level functions to fit dispersion estimates |

estimateSizeFactors | Estimate the size factors for a 'DESeqDataSet' |

estimateSizeFactorsForMatrix | Low-level function to estimate size factors with robust... |

fpkm | FPKM: fragments per kilobase per million mapped fragments |

fpm | FPM: fragments per million mapped fragments |

lfcShrink | Shrink log2 fold changes |

makeExampleDESeqDataSet | Make a simulated DESeqDataSet |

nbinomLRT | Likelihood ratio test (chi-squared test) for GLMs |

nbinomWaldTest | Wald test for the GLM coefficients |

normalizationFactors | Accessor functions for the normalization factors in a... |

normalizeGeneLength | Normalize for gene length |

normTransform | Normalized counts transformation |

plotCounts | Plot of normalized counts for a single gene |

plotDispEsts | Plot dispersion estimates |

plotMA | MA-plot from base means and log fold changes |

plotPCA | Sample PCA plot for transformed data |

plotSparsity | Sparsity plot |

priorInfo | Accessors for the 'priorInfo' slot of a DESeqResults object. |

replaceOutliers | Replace outliers with trimmed mean |

results | Extract results from a DESeq analysis |

rlog | Apply a 'regularized log' transformation |

show | Show method for DESeqResults objects |

sizeFactors | Accessor functions for the 'sizeFactors' information in a... |

summary | Summarize DESeq results |

unmix | Unmix samples using loss in a variance stabilized space |

varianceStabilizingTransformation | Apply a variance stabilizing transformation (VST) to the... |

vst | Quickly estimate dispersion trend and apply a variance... |

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