Man pages for DESeq
Differential gene expression analysis based on the negative binomial distribution
| adjustScvForBias | Adjust an SCV value for the bias arising when it is... |
| conditions | Accessor functions for the 'conditions' information in a... |
| CountDataSet-class | Class "CountDataSet" - a container for count data from HTS... |
| counts | Accessors for the 'counts' slot of a CountDataSet object. |
| dispTable | Accessor function for the dispTable information in a... |
| estimateDispersions | Estimate and fit dispersions for a CountDataSet. |
| estimateSizeFactors | Estimate the size factors for a CountDataSet |
| estimateSizeFactorsForMatrix | Low-level function to estimate size factors with robust... |
| estimateVarianceFunctions | REMOVED |
| fitInfo | Accessor function for the fitInfo objects in a CountDataSet |
| fitNbinomGLMs | Fit a generalized linear model (GLM) for each gene. |
| fitNbinomGLMsForMatrix | Fit negative binomial GLMs to a count matrix. |
| getBaseMeansAndVariances | Perform row-wise estimates of base-level means and variances... |
| getVarianceStabilizedData | Apply a variance stabilizing transformation (VST) to the... |
| makeExampleCountDataSet | make a simple example CountDataSet with random data |
| nbinomGLMTest | Perform chi-squared tests comparing two sets of GLM fits |
| nbinomTest | Test for differences between the base means for two... |
| nbinomTestForMatrices | Perform row-wise tests for differences between the base means... |
| nbkd.sf | GLM family for a negative binomial with known dispersion and... |
| newCountDataSet | Create a CountDataSet object |
| newCountDataSetFromHTSeqCount | Create a new CountDataSet from count files generated with... |
| plotDispEsts | Plot dispersion estimates and fitted values |
| plotMA | Makes a so-called "MA-plot" |
| plotPCA | Sample PCA plot from variance-stabilized data |
| residualsEcdfPlot | REMOVED |
| scvPlot | REMOVED |
| sizeFactors | Accessor functions for the 'sizeFactors' information in a... |
| varianceFitDiagnostics | REMOVED |
