Man pages for aghozlane/DESeq2shaman
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 SummarizedExperiment or... |
| counts | Accessors for the 'counts' slot of a DESeqDataSet object. |
| DESeq | Differential expression analysis based on the Negative... |
| DESeqDataSet | DESeqDataSet object and constructors |
| DESeqResults | DESeqResults 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 |
| 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... |
| plotCounts | Plot of normalized counts for a single gene on log scale |
| plotDispEsts | Plot dispersion estimates |
| plotMA | MA-plot from base means and log fold changes |
| plotPCA | Sample PCA plot from variance-stabilized data |
| 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 |
| varianceStabilizingTransformation | Apply a variance stabilizing transformation (VST) to the... |
