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A B C D E G L M N P Q R S T W misc
| edgeR-package | Empirical analysis of digital gene expression data in R |
| adjustedProfileLik | Compute Cox-Reid Adjusted Profile Likelihood for Negative Binomial GLMs |
| approx.expected.info | Approximate Expected Information (Fisher Information) |
| as.data.frame.TopTags | Turn a TopTags Object into a Dataframe |
| as.matrix.DGEList | Turn a DGEList Object into a Matrix |
| betaApproxNBTest | An Approximate Exact Test for Differences between Two Negative Binomial Groups |
| binCMLDispersion | Estimate Common Dispersion for Negative Binomial GLMs in Bins of Genes Sorted by Overall Abundance |
| binGLMDispersion | Estimate Common Dispersion for Negative Binomial GLMs in Bins of Genes Sorted by Overall Abundance |
| binMeanVar | Explore the mean-variance relationship for DGE data |
| binomTest | Exact Binomial Tests for Comparing Two Digital Libraries |
| 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 |
| cpm | Calculate Counts per Million from DGEList or Matrix Object |
| cutWithMinN | Cut numeric vector into non-empty intervals |
| decideTestsDGE | Multiple Testing Across Genes and Contrasts |
| designAsFactor | Fit Negative Binomial Generalized Linear Model to Multiple Response Vectors |
| deviances.function | Fit Negative Binomial Generalized Linear Model to Multiple Response Vectors |
| DGEExact-class | differential expression of Digital Gene Expression data - class |
| DGEGLM-class | Digital Gene Expression Generalized Linear Model results - class |
| DGEList | DGEList Constructor |
| DGEList-class | Digital Gene Expression data - class |
| DGELRT-class | Digital Gene Expression Likelihood Ratio Test data and results - class |
| dglmStdResid | Visualize the mean-variance relationship in DGE data using standardized residuals |
| dim.DGEExact | Retrieve the Dimensions of a DGEList, DGEExact, DGEGLM, DGELRT or TopTags Object |
| dim.DGEGLM | Retrieve the Dimensions of a DGEList, DGEExact, DGEGLM, DGELRT or TopTags Object |
| dim.DGEList | Retrieve the Dimensions of a DGEList, DGEExact, DGEGLM, DGELRT or TopTags Object |
| dim.DGELRT | Retrieve the Dimensions of a DGEList, DGEExact, DGEGLM, DGELRT or TopTags Object |
| dim.TopTags | Retrieve the Dimensions of a DGEList, DGEExact, DGEGLM, DGELRT or TopTags Object |
| dimnames.DGEList | Retrieve the Dimension Names of a DGEList Object |
| dimnames<-.DGEList | Retrieve the Dimension Names of a DGEList Object |
| dispBinTrend | Estimate Dispersions with an Abundance-Dependent Trend for Negative Binomial GLMs |
| dispCoxReid | Estimate Common Dispersion for Negative Binomial GLMs |
| dispCoxReidInterpolateTagwise | Estimate Tagwise Dispersion for Negative Binomial GLMs by Cox-Reid Adjusted Profile Likelihood |
| dispCoxReidPowerTrend | Estimate Dispersion Trend for Negative Binomial GLMs |
| dispCoxReidSplineTrend | Estimate Dispersion Trend for Negative Binomial GLMs |
| dispDeviance | Estimate Common Dispersion for Negative Binomial GLMs |
| dispPearson | Estimate Common Dispersion for Negative Binomial GLMs |
| 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 |
| estimateExonGenewiseDisp | Estimate Genewise Dispersions from Exon-Level Count Data |
| estimateGLMCommonDisp | Estimate Common Dispersion for Negative Binomial GLMs |
| estimateGLMCommonDisp.default | Estimate Common Dispersion for Negative Binomial GLMs |
| estimateGLMCommonDisp.DGEList | Estimate Common Dispersion for Negative Binomial GLMs |
| estimateGLMTagwiseDisp | Estimate Empirical Bayes Tagwise Dispersions for Negative Binomial GLMs |
| estimateGLMTagwiseDisp.default | Estimate Empirical Bayes Tagwise Dispersions for Negative Binomial GLMs |
| estimateGLMTagwiseDisp.DGEList | Estimate Empirical Bayes Tagwise Dispersions for Negative Binomial GLMs |
| estimateGLMTrendedDisp | Estimate Trended Dispersion for Negative Binomial GLMs |
| estimateGLMTrendedDisp.default | Estimate Trended Dispersion for Negative Binomial GLMs |
| estimateGLMTrendedDisp.DGEList | Estimate Trended Dispersion for Negative Binomial GLMs |
| estimatePs | Estimate Expression Levels |
| estimateSmoothing | Estimate the Prior Weight for Tagwise Dispersions |
| estimateTagwiseDisp | Estimate Empirical Bayes Tagwise Dispersion Values |
| exactTest | Exact Tests for Differences between Two Groups of Negative-Binomial Counts |
| exactTestBetaApprox | Exact Tests for Differences between Two Groups of Negative-Binomial Counts |
| exactTestByDeviance | Exact Tests for Differences between Two Groups of Negative-Binomial Counts |
| exactTestBySmallP | Exact Tests for Differences between Two Groups of Negative-Binomial Counts |
| exactTestDoubleTail | Exact Tests for Differences between Two Groups of Negative-Binomial Counts |
| expandAsMatrix | expandAsMatrix |
| getCounts | Extract Specified Component of a DGEList Object |
| getDispersion | Extract Specified Component of a DGEList Object |
| getDispersions | Visualize the mean-variance relationship in DGE data using standardized residuals |
| getOffset | Extract Specified Component of a DGEList Object |
| getPriorN | Get a Recommended Value for Prior N from DGEList Object |
| glmFit | Fit negative binomial generalized linear model for each transcript |
| glmFit.default | Fit negative binomial generalized linear model for each transcript |
| glmFit.DGEList | Fit negative binomial generalized linear model for each transcript |
| glmLRT | Fit negative binomial generalized linear model for each transcript |
| gof | Goodness of Fit Tests for Multiple GLM Fits |
| goodTuring | Good-Turing Frequency Estimation |
| goodTuringProportions | Good-Turing Frequency Estimation |
| length.DGEExact | Retrieve the Dimensions of a DGEList, DGEExact, DGEGLM, DGELRT or TopTags Object |
| length.DGEGLM | Retrieve the Dimensions of a DGEList, DGEExact, DGEGLM, DGELRT or TopTags Object |
| length.DGEList | Retrieve the Dimensions of a DGEList, DGEExact, DGEGLM, DGELRT or TopTags Object |
| length.DGELRT | Retrieve the Dimensions of a DGEList, DGEExact, DGEGLM, DGELRT or TopTags Object |
| length.TopTags | Retrieve the Dimensions of a DGEList, DGEExact, DGEGLM, DGELRT or TopTags Object |
| logLikDerP | Log-Likelihood for Proportion |
| maPlot | Plots Log-Fold Change versus Log-Concentration (or, M versus A) for Count Data |
| maximizeInterpolant | Maximize a function given a table of values by spline interpolation. |
| mglm | Fit Negative Binomial Generalized Linear Model to Multiple Response Vectors |
| mglmLevenberg | Fit Negative Binomial Generalized Linear Model to Multiple Response Vectors |
| mglmLS | Fit Negative Binomial Generalized Linear Model to Multiple Response Vectors |
| mglmOneGroup | Fit Negative Binomial Generalized Linear Model to Multiple Response Vectors |
| mglmOneWay | Fit Negative Binomial Generalized Linear Model to Multiple Response Vectors |
| mglmSimple | Fit Negative Binomial Generalized Linear Model to Multiple Response Vectors |
| movingAverageByCol | Moving Average Smoother of Matrix Columns |
| 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. |
| plotExonUsage | Create a Plot of Exon Usage from Exon-Level Count Data |
| plotMDS.DGEList | Multidimensional scaling plot of digital gene expression profiles |
| plotMeanVar | Explore the mean-variance relationship for DGE 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 |
| readDGE | Read and Merge a Set of Files Containing DGE Data |
| show-method | differential expression of Digital Gene Expression data - class |
| show-method | Digital Gene Expression Generalized Linear Model results - class |
| show-method | Digital Gene Expression Likelihood Ratio Test data and results - class |
| show-method | Table of the Top Differentially Expressed Tags |
| spliceVariants | Identify Genes with Splice Variants |
| 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, DGEGLM, DGEExact and DGELRT Objects |
| systematicSubset | Take a systematic subset of indices. |
| thinCounts | Binomial Thinning of Counts |
| 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. |
| weightedComLik | Weighted Common Log-Likelihood |
| weightedComLikMA | Weighted Common Log-Likelihood |
| weightedCondLogLikDerDelta | Weighted Conditional Log-Likelihood in Terms of Delta |
| [.DGEExact | Subset DGEList, DGEGLM, DGEExact and DGELRT Objects |
| [.DGEGLM | Subset DGEList, DGEGLM, DGEExact and DGELRT Objects |
| [.DGEList | Subset DGEList, DGEGLM, DGEExact and DGELRT Objects |
| [.DGELRT | Subset DGEList, DGEGLM, DGEExact and DGELRT Objects |
| [.TopTags | Table of the Top Differentially Expressed Tags |