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A B C D E F G H K L M N O P Q R S T V W Z misc
| edgeR-package | Empirical analysis of digital gene expression data in R |
| addPriorCount | Add a prior count |
| adjustedProfileLik | Adjusted Profile Likelihood for the Negative Binomial Dispersion Parameter |
| as.data.frame.DGEExact | Turn a TopTags Object into a Dataframe |
| as.data.frame.DGELRT | Turn a TopTags Object into a Dataframe |
| as.data.frame.TopTags | Turn a TopTags Object into a Dataframe |
| as.matrix.CompressedMatrix | makeCompressedMatrix |
| as.matrix.DGEList | Turn a DGEList Object into a Matrix |
| aveLogCPM | Average Log Counts Per Million |
| aveLogCPM.default | Average Log Counts Per Million |
| aveLogCPM.DGEGLM | Average Log Counts Per Million |
| aveLogCPM.DGEList | Average Log Counts Per Million |
| aveLogCPM.SummarizedExperiment | Average Log Counts Per Million |
| binMeanVar | Explore the Mean-Variance Relationship for DGE Data |
| binomTest | Exact Binomial Tests for Comparing Two Digital Libraries |
| calcNormFactors | Calculate Normalization Factors to Align Columns of a Count Matrix |
| calcNormFactors.default | Calculate Normalization Factors to Align Columns of a Count Matrix |
| calcNormFactors.DGEList | Calculate Normalization Factors to Align Columns of a Count Matrix |
| calcNormFactors.SummarizedExperiment | Calculate Normalization Factors to Align Columns of a Count Matrix |
| calcNormOffsetsforChIP | Normalize ChIP-Seq Read Counts to Input and Test for Enrichment |
| camera.DGEList | Competitive Gene Set Tests for Digital Gene Expression Data |
| catchKallisto | Process Kallisto or Salmon Output |
| catchSalmon | Process Kallisto or Salmon Output |
| cbind | Combine DGEList Objects |
| cbind.CompressedMatrix | makeCompressedMatrix |
| cbind.DGEList | Combine DGEList Objects |
| commonCondLogLikDerDelta | Conditional Log-Likelihoods in Terms of Delta |
| CompressedMatrix | makeCompressedMatrix |
| CompressedMatrix-class | makeCompressedMatrix |
| condLogLikDerDelta | Conditional Log-Likelihood of the Dispersion for a Single Group of Replicate Libraries |
| condLogLikDerSize | Conditional Log-Likelihood of the Dispersion for a Single Group of Replicate Libraries |
| cpm | Counts per Million or Reads per Kilobase per Million |
| cpm.default | Counts per Million or Reads per Kilobase per Million |
| cpm.DGEGLM | Counts per Million or Reads per Kilobase per Million |
| cpm.DGEList | Counts per Million or Reads per Kilobase per Million |
| cpm.DGELRT | Counts per Million or Reads per Kilobase per Million |
| cpm.SummarizedExperiment | Counts per Million or Reads per Kilobase per Million |
| cpmByGroup | Counts per Million or Reads per Kilobase per Million |
| cpmByGroup.default | Counts per Million or Reads per Kilobase per Million |
| cpmByGroup.DGEList | Counts per Million or Reads per Kilobase per Million |
| cpmByGroup.SummarizedExperiment | Counts per Million or Reads per Kilobase per Million |
| cutWithMinN | Cut numeric vector into non-empty intervals |
| decideTests.DGEExact | Multiple Testing Across Genes and Contrasts |
| decideTests.DGELRT | Multiple Testing Across Genes and Contrasts |
| decideTestsDGE | Multiple Testing Across Genes and Contrasts |
| designAsFactor | Fit Negative Binomial Generalized Linear Models to Multiple Response Vectors: Low Level Functions |
| 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 |
| diffSpliceDGE | Test for Differential Exon Usage |
| dim.CompressedMatrix | makeCompressedMatrix |
| 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.DGEExact | Retrieve the Dimension Names of a DGE Object |
| dimnames.DGEGLM | Retrieve the Dimension Names of a DGE Object |
| dimnames.DGEList | Retrieve the Dimension Names of a DGE Object |
| dimnames.DGELRT | Retrieve the Dimension Names of a DGE Object |
| dimnames.TopTags | Retrieve the Dimension Names of a DGE Object |
| dimnames<-.DGEExact | Retrieve the Dimension Names of a DGE Object |
| dimnames<-.DGEGLM | Retrieve the Dimension Names of a DGE Object |
| dimnames<-.DGEList | Retrieve the Dimension Names of a DGE Object |
| dimnames<-.DGELRT | Retrieve the Dimension Names of a DGE Object |
| dispBinTrend | Estimate Dispersion Trend by Binning for NB GLMs |
| dispCoxReid | Estimate Common Dispersion for Negative Binomial GLMs |
| dispCoxReidInterpolateTagwise | Estimate Genewise 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 |
| dropEmptyLevels | Drop Levels of a Factor that Never Occur |
| edgeR | Empirical analysis of digital gene expression data in R |
| edgeRUsersGuide | View edgeR User's Guide |
| effectiveLibSizes | Effective Library Sizes |
| effectiveLibSizes.default | Effective Library Sizes |
| effectiveLibSizes.DGEGLM | Effective Library Sizes |
| effectiveLibSizes.DGEList | Effective Library Sizes |
| effectiveLibSizes.DGELRT | Effective Library Sizes |
| equalizeLibSizes | Equalize Library Sizes by Quantile-to-Quantile Normalization |
| equalizeLibSizes.default | Equalize Library Sizes by Quantile-to-Quantile Normalization |
| equalizeLibSizes.DGEList | Equalize Library Sizes by Quantile-to-Quantile Normalization |
| estimateCommonDisp | Estimate Common Negative Binomial Dispersion by Conditional Maximum Likelihood |
| estimateCommonDisp.default | Estimate Common Negative Binomial Dispersion by Conditional Maximum Likelihood |
| estimateCommonDisp.DGEList | Estimate Common Negative Binomial Dispersion by Conditional Maximum Likelihood |
| estimateDisp | Estimate Common, Trended and Tagwise Negative Binomial dispersions by weighted likelihood empirical Bayes |
| estimateDisp.default | Estimate Common, Trended and Tagwise Negative Binomial dispersions by weighted likelihood empirical Bayes |
| estimateDisp.DGEList | Estimate Common, Trended and Tagwise Negative Binomial dispersions by weighted likelihood empirical Bayes |
| estimateDisp.SummarizedExperiment | Estimate Common, Trended and Tagwise Negative Binomial dispersions by weighted likelihood empirical Bayes |
| 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 |
| estimateGLMRobustDisp | Empirical Robust Bayes Tagwise Dispersions for Negative Binomial GLMs using Observation Weights |
| estimateGLMTagwiseDisp | Empirical Bayes Tagwise Dispersions for Negative Binomial GLMs |
| estimateGLMTagwiseDisp.default | Empirical Bayes Tagwise Dispersions for Negative Binomial GLMs |
| estimateGLMTagwiseDisp.DGEList | 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 |
| estimateTagwiseDisp | Estimate Empirical Bayes Tagwise Dispersion Values |
| estimateTagwiseDisp.default | Estimate Empirical Bayes Tagwise Dispersion Values |
| estimateTagwiseDisp.DGEList | Estimate Empirical Bayes Tagwise Dispersion Values |
| estimateTrendedDisp | Estimate Empirical Bayes Trended Dispersion Values |
| estimateTrendedDisp.default | Estimate Empirical Bayes Trended Dispersion Values |
| estimateTrendedDisp.DGEList | Estimate Empirical Bayes Trended 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 |
| filterByExpr | Filter Genes By Expression Level |
| filterByExpr.default | Filter Genes By Expression Level |
| filterByExpr.DGEList | Filter Genes By Expression Level |
| filterByExpr.SummarizedExperiment | Filter Genes By Expression Level |
| fry.DGEList | Self-contained Gene Set Tests for Digital Gene Expression Data |
| getCounts | Extract Specified Component of a DGEList Object |
| getDispersion | Extract Specified Component of a DGEList Object |
| getOffset | Extract Specified Component of a DGEList Object |
| getPriorN | Get a Recommended Value for Prior N from DGEList Object |
| gini | Gini dispersion index |
| glmFit | Genewise Negative Binomial Generalized Linear Models |
| glmFit.default | Genewise Negative Binomial Generalized Linear Models |
| glmFit.DGEList | Genewise Negative Binomial Generalized Linear Models |
| glmFit.SummarizedExperiment | Genewise Negative Binomial Generalized Linear Models |
| glmLRT | Genewise Negative Binomial Generalized Linear Models |
| glmQLFit | Genewise Negative Binomial Generalized Linear Models with Quasi-likelihood Tests |
| glmQLFit.default | Genewise Negative Binomial Generalized Linear Models with Quasi-likelihood Tests |
| glmQLFit.DGEList | Genewise Negative Binomial Generalized Linear Models with Quasi-likelihood Tests |
| glmQLFit.SummarizedExperiment | Genewise Negative Binomial Generalized Linear Models with Quasi-likelihood Tests |
| glmQLFTest | Genewise Negative Binomial Generalized Linear Models with Quasi-likelihood Tests |
| glmTreat | Test for Differential Expression Relative to a Threshold |
| goana.DGEExact | Gene Ontology or KEGG Analysis of Differentially Expressed Genes |
| goana.DGELRT | Gene Ontology or KEGG Analysis of Differentially Expressed Genes |
| gof | Goodness of Fit Tests for Multiple GLM Fits |
| goodTuring | Good-Turing Frequency Estimation |
| goodTuringPlot | Good-Turing Frequency Estimation |
| goodTuringProportions | Good-Turing Frequency Estimation |
| head.DGEExact | Return the First to Last Part of a Data Object |
| head.DGEGLM | Return the First to Last Part of a Data Object |
| head.DGEList | Return the First to Last Part of a Data Object |
| head.DGELRT | Return the First to Last Part of a Data Object |
| head.TopTags | Return the First to Last Part of a Data Object |
| kegga.DGEExact | Gene Ontology or KEGG Analysis of Differentially Expressed Genes |
| kegga.DGELRT | Gene Ontology or KEGG Analysis of Differentially Expressed Genes |
| length.CompressedMatrix | makeCompressedMatrix |
| locfitByCol | Locally Weighted Mean By Column |
| loessByCol | Locally Weighted Mean By Column |
| makeCompressedMatrix | makeCompressedMatrix |
| 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. |
| maximizeQuadratic | Maximize a function given a table of values by quadratic interpolation. |
| mglm | Fit Negative Binomial Generalized Linear Models to Multiple Response Vectors: Low Level Functions |
| mglmLevenberg | Fit Negative Binomial Generalized Linear Models to Multiple Response Vectors: Low Level Functions |
| mglmOneGroup | Fit Negative Binomial Generalized Linear Models to Multiple Response Vectors: Low Level Functions |
| mglmOneWay | Fit Negative Binomial Generalized Linear Models to Multiple Response Vectors: Low Level Functions |
| modelMatrixMeth | Construct Design Matrix for edgeR Analysis of Methylation Count Data |
| movingAverageByCol | Moving Average Smoother of Matrix Columns |
| mroast.DGEList | Self-contained Gene Set Tests for Digital Gene Expression Data |
| nbinomDeviance | Negative Binomial Deviance |
| nbinomUnitDeviance | Negative Binomial Unit Deviance |
| nearestReftoX | Find Nearest Element of Reference for each Element of X |
| nearestTSS | Find Nearest Transcriptional Start Site |
| normalizeChIPtoInput | Normalize ChIP-Seq Read Counts to Input and Test for Enrichment |
| Ops.CompressedMatrix | makeCompressedMatrix |
| plotBCV | Plot Biological Coefficient of Variation |
| plotExonUsage | Create a Plot of Exon Usage from Exon-Level Count Data |
| plotMD.DGEExact | Mean-Difference Plot of Count Data |
| plotMD.DGEGLM | Mean-Difference Plot of Count Data |
| plotMD.DGEList | Mean-Difference Plot of Count Data |
| plotMD.DGELRT | Mean-Difference Plot of Count Data |
| plotMD.SummarizedExperiment | Mean-Difference Plot of Count Data |
| plotMDS.DGEList | Multidimensional scaling plot of distances between digital gene expression profiles |
| plotMDS.SummarizedExperiment | Multidimensional scaling plot of distances between digital gene expression profiles |
| plotMeanVar | Explore the Mean-Variance Relationship for DGE Data |
| plotMeanVar2 | Plot Mean-Variance Relationship in DGE Data Using Standardized Residuals |
| plotQLDisp | Plot the quasi-likelihood dispersion |
| plotSmear | Smear plot |
| plotSpliceDGE | Differential splicing plot |
| predFC | Predictive log-fold changes |
| predFC.default | Predictive log-fold changes |
| predFC.DGEList | Predictive log-fold changes |
| predFC.SummarizedExperiment | Predictive log-fold changes |
| processAmplicons | Process raw data from pooled genetic sequencing screens |
| q2qnbinom | Quantile to Quantile Mapping between Negative-Binomial Distributions |
| q2qpois | Quantile to Quantile Mapping between Negative-Binomial Distributions |
| rbind.CompressedMatrix | makeCompressedMatrix |
| rbind.DGEList | Combine DGEList Objects |
| read10X | Read 10X Genomics Files |
| readBismark2DGE | Read Bismark Coverage Files |
| readDGE | Read and Merge a Set of Files Containing Count Data |
| roast.DGEList | Self-contained Gene Set Tests for Digital Gene Expression Data |
| romer.DGEList | Rotation Gene Set Enrichment for Digital Gene Expression Data |
| rowsum.DGEList | Sum Over Groups of Genes |
| rowsum.SummarizedExperiment | Sum Over Groups of Genes |
| rpkm | Counts per Million or Reads per Kilobase per Million |
| rpkm.default | Counts per Million or Reads per Kilobase per Million |
| rpkm.DGEGLM | Counts per Million or Reads per Kilobase per Million |
| rpkm.DGEList | Counts per Million or Reads per Kilobase per Million |
| rpkm.DGELRT | Counts per Million or Reads per Kilobase per Million |
| rpkm.SummarizedExperiment | Counts per Million or Reads per Kilobase per Million |
| rpkmByGroup | Counts per Million or Reads per Kilobase per Million |
| rpkmByGroup.default | Counts per Million or Reads per Kilobase per Million |
| rpkmByGroup.DGEList | Counts per Million or Reads per Kilobase per Million |
| rpkmByGroup.SummarizedExperiment | Counts per Million or Reads per Kilobase per Million |
| scaleOffset | Scale offsets |
| scaleOffset.default | Scale offsets |
| scaleOffset.DGEList | Scale offsets |
| SE2DGEList | SummarizedExperiment to DGEList |
| 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 Genes/Tags |
| spliceVariants | Identify Genes with Splice Variants |
| splitIntoGroups | Split the Counts or Pseudocounts from a DGEList Object According To Group |
| splitIntoGroups.default | Split the Counts or Pseudocounts from a DGEList Object According To Group |
| splitIntoGroups.DGEList | 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 |
| sumTechReps | Sum Over Replicate Samples |
| sumTechReps.default | Sum Over Replicate Samples |
| sumTechReps.DGEList | Sum Over Replicate Samples |
| sumTechReps.SummarizedExperiment | Sum Over Replicate Samples |
| systematicSubset | Take a systematic subset of indices. |
| tail.DGEExact | Return the First to Last Part of a Data Object |
| tail.DGEGLM | Return the First to Last Part of a Data Object |
| tail.DGEList | Return the First to Last Part of a Data Object |
| tail.DGELRT | Return the First to Last Part of a Data Object |
| tail.TopTags | Return the First to Last Part of a Data Object |
| thinCounts | Binomial or Multinomial Thinning of Counts |
| topSpliceDGE | Top table of differentially spliced genes or exons |
| topTags | Table of the Top Differentially Expressed Genes/Tags |
| TopTags-class | Table of the Top Differentially Expressed Genes/Tags |
| validDGEList | Check for Valid DGEList object |
| voomLmFit | Apply voom-lmFit Pipeline While Accounting for Loss of Residual DF Due to Exact Zeros |
| weightedCondLogLikDerDelta | Weighted Conditional Log-Likelihood in Terms of Delta |
| WLEB | Weighted Likelihood Empirical Bayes |
| zscoreNBinom | Z-score Equivalents of Negative Binomial Deviate |
| [.CompressedMatrix | makeCompressedMatrix |
| [.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 | Subset DGEList, DGEGLM, DGEExact and DGELRT Objects |
| [<-.CompressedMatrix | makeCompressedMatrix |