edgeR-package |
Empirical analysis of digital gene expression data in R |
alpha.approxeb |
Estimate the Prior Weight, Alpha |
approx.expected.info |
Approximate Expected Information (Fisher Information) |
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 |
de4DGE |
Compute Moderated Differential Expression Scores for Digital Gene Expression (DGE) Data |
de4DGEList-class |
differential expression for Digital Gene Expression data - class |
deDGE |
Compute Moderated Differential Expression Scores for Digital Gene Expression (DGE) Data |
deDGEList-class |
differential expression of Digital Gene Expression data - class |
DGEList |
DGEList Constructor |
DGEList-class |
Digital Gene Expression data - class |
EBList-class |
Differential Expression of Digital Gene Expression data - class |
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 |
estimateDispIter |
Normalizes a Dataset Using Quantile Adjustment and Iteratively Estimates the Dispersion Parameter |
estimatePs |
Estimate Expression Levels |
estimateSmoothing |
Estimate the Prior Weight |
estimateTagwiseDisp |
Maximizes the Negative Binomial Weighted Conditional Likelihood |
exactTest |
An Exact Test for Differences between Two Negative Binomial Groups |
exactTest.matrix |
An Exact Test for Differences between Two Negative Binomial Groups |
findMaxD2 |
Maximizes the Negative Binomial Likelihood |
getCounts |
Extract Table of Counts from DGEList Object |
interpolateHelper |
Quantile Adjustment Interpolator |
logLikDerP |
Log-Likelihood for Proportion |
maPlot |
Plots Log-Fold Change versus Log-Concentration (or, M versus A) for Count Data |
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. |
plotFC |
Plots log-Fold Change versus log-Concentration (or, M versus A) for Count 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 |
quantileAdjust |
Normalizes a Dataset by Using a Quantile Adjustment |
readDGE |
Read and Merge a Set of Files Containing DGE Data |
show,de4DGEList-method |
differential expression for Digital Gene Expression data - class |
show,deDGEList-method |
differential expression of Digital Gene Expression data - class |
show,EBList-method |
Differential Expression of Digital Gene Expression data - class |
show,TopTags-method |
Table of the Top Differentially Expressed Tags |
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 Objects |
tau2.0.objective |
Objective Function for Tau2 |
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. |
weightedCondLogLikDerDelta |
Weighted Conditional Log-Likelihood in Terms of Delta |
[.DGEList |
Subset DGEList Objects |
[.TopTags |
Table of the Top Differentially Expressed Tags |