A B C D E F G K L M N 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.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 |
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 |
calcNormOffsetsforChIP | Normalize ChIP-Seq Read Counts to Input and Test for Enrichment |
camera.DGEList | Competitive Gene Set Test for Digital Gene Expression Data Accounting for Inter-gene Correlation |
commonCondLogLikDerDelta | Conditional Log-Likelihoods in Terms of Delta |
compressedMatrix | 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.DGEList | 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 Model 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 |
dglmStdResid | Visualize the mean-variance relationship in DGE data using standardized residuals |
diffSpliceDGE | Test for Differential Exon Usage |
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 |
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 |
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 |
fry.DGEList | Rotation Gene Set Tests for Digital Gene Expression Data |
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 |
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 |
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 |
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 |
kegga.DGEExact | Gene Ontology or KEGG Analysis of Differentially Expressed Genes |
kegga.DGELRT | Gene Ontology or KEGG Analysis of Differentially Expressed Genes |
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 Model to Multiple Response Vectors: Low Level Functions |
mglmLevenberg | Fit Negative Binomial Generalized Linear Model to Multiple Response Vectors: Low Level Functions |
mglmOneGroup | Fit Negative Binomial Generalized Linear Model to Multiple Response Vectors: Low Level Functions |
mglmOneWay | Fit Negative Binomial Generalized Linear Model to Multiple Response Vectors: Low Level Functions |
movingAverageByCol | Moving Average Smoother of Matrix Columns |
mroast.DGEList | Rotation Gene Set Tests for Digital Gene Expression Data |
nbinomDeviance | Negative Binomial Deviance |
nbinomUnitDeviance | Negative Binomial Deviance |
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 |
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 |
plotMDS.DGEList | Multidimensional scaling plot of distances between digital gene expression profiles |
plotMeanVar | Explore the mean-variance relationship for DGE data |
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 |
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 |
readDGE | Read and Merge a Set of Files Containing Count Data |
roast.DGEList | Rotation Gene Set Tests for Digital Gene Expression Data |
romer.DGEList | Rotation Gene Set Tests for Digital Gene Expression Data |
rpkm | Counts per Million or Reads per Kilobase per Million |
rpkm.default | Counts per Million or Reads per Kilobase per Million |
rpkm.DGEList | Counts per Million or Reads per Kilobase per Million |
scaleOffset | Scale offsets |
scaleOffset.default | Scale offsets |
scaleOffset.DGEList | Scale offsets |
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 |
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 |
systematicSubset | Take a systematic subset of indices. |
thinCounts | Binomial or Multinomial Thinning of Counts |
topSpliceDGE | Top table of differentially spliced genes or exons |
topTags | Table of the Top Differentially Expressed Tags |
TopTags-class | Table of the Top Differentially Expressed Tags |
validDGEList | Check for Valid DGEList object |
weightedCondLogLikDerDelta | Weighted Conditional Log-Likelihood in Terms of Delta |
WLEB | Calculate Weighted Likelihood Empirical Bayes Estimates |
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 |