A B C D E G L M N P Q R S T W Z 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 | Calculate Normalization Factors to Align Columns of a Count Matrix |
calcNormOffsetsforChIP | Normalize ChIP-Seq Read Counts to Input and Test for Enrichment |
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.DGEExact | Retrieve the Dimension Names of a DGEList Object |
dimnames.DGEGLM | Retrieve the Dimension Names of a DGEList Object |
dimnames.DGEList | Retrieve the Dimension Names of a DGEList Object |
dimnames.TopTags | Retrieve the Dimension Names of a DGEList Object |
dimnames<-.DGEExact | Retrieve the Dimension Names of a DGEList Object |
dimnames<-.DGEGLM | Retrieve the Dimension Names of a DGEList Object |
dimnames<-.DGEList | Retrieve the Dimension Names of a DGEList Object |
dimnames<-.TopTags | 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 |
edgeRUsersGuide | View edgeR User's Guide |
equalizeLibSizes | Quantile Adjustment to Equalize Library Sizes for a Fixed Value of the Dispersion Parameter |
estimateCommonDisp | Estimate Common Negative Binomial Dispersion by Conditional Maximum 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 |
estimateTrendedDisp | 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 |
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 | Genewise Negative Binomial Generalized Linear Mdels |
glmFit.default | Genewise Negative Binomial Generalized Linear Mdels |
glmFit.DGEList | Genewise Negative Binomial Generalized Linear Mdels |
glmLRT | Genewise Negative Binomial Generalized Linear Mdels |
glmQLFTest | Genewise Negative Binomial Generalized Linear Mdels |
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. |
maximizeQuadratic | Maximize a function given a table of values by quadratic 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. |
normalizeChIPtoInput | Normalize ChIP-Seq Read Counts to Input and Test for Enrichment |
plotBCV | Plot Biological Coefficient of Variation |
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 |
predFC | Predictive log fold changes for RNASeq data |
predFC.default | Predictive log fold changes for RNASeq data |
predFC.DGEList | Predictive log fold changes for RNASeq 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 or Multinomial 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 |
zscoreNBinom | Z-score Equivalents of Negative Binomial Deviate |
[.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 |