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Version
3.14.0
3.12.1
3.10.5
3.8.6
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Version
3.14.0
License
GPL (>=2)
Maintainer
Yunshun Chen
Last Published
April 19th, 2016
Functions in edgeR (3.14.0)
Search functions
dropEmptyLevels
Drop Levels of a Factor that Never Occur
WLEB
Calculate Weighted Likelihood Empirical Bayes Estimates
estimateGLMTagwiseDisp
Empirical Bayes Tagwise Dispersions for Negative Binomial GLMs
gini
Gini dispersion index
gof
Goodness of Fit Tests for Multiple GLM Fits
dispCoxReidSplineTrend
Estimate Dispersion Trend for Negative Binomial GLMs
nbinomDeviance
Negative Binomial Deviance
DGELRT-class
Digital Gene Expression Likelihood Ratio Test data and results - class
DGEExact-class
differential expression of Digital Gene Expression data - class
calcNormFactors
Calculate Normalization Factors to Align Columns of a Count Matrix
predFC
Predictive log-fold changes
edgeR-package
Empirical analysis of digital gene expression data in R
aveLogCPM
Average Log Counts Per Million
decideTestsDGE
Multiple Testing Across Genes and Contrasts
loessByCol
Locally Weighted Mean By Column
plotExonUsage
Create a Plot of Exon Usage from Exon-Level Count Data
dim
Retrieve the Dimensions of a DGEList, DGEExact, DGEGLM, DGELRT or TopTags Object
plotSpliceDGE
Differential splicing plot
processAmplicons
Process raw data from pooled genetic sequencing screens
dispCoxReidInterpolateTagwise
Estimate Genewise Dispersion for Negative Binomial GLMs by Cox-Reid Adjusted Profile Likelihood
binomTest
Exact Binomial Tests for Comparing Two Digital Libraries
movingAverageByCol
Moving Average Smoother of Matrix Columns
expandAsMatrix
expandAsMatrix
splitIntoGroups
Split the Counts or Pseudocounts from a DGEList Object According To Group
estimateGLMCommonDisp
Estimate Common Dispersion for Negative Binomial GLMs
weightedCondLogLikDerDelta
Weighted Conditional Log-Likelihood in Terms of Delta
topSpliceDGE
Top table of differentially spliced genes or exons
estimateTagwiseDisp
Estimate Empirical Bayes Tagwise Dispersion Values
plotMDS.DGEList
Multidimensional scaling plot of distances between digital gene expression profiles
diffSpliceDGE
Test for Differential Exon Usage
meanvar
Explore the mean-variance relationship for DGE data
glmFit
Genewise Negative Binomial Generalized Linear Models
goodTuring
Good-Turing Frequency Estimation
normalizeChIPtoInput
Normalize ChIP-Seq Read Counts to Input and Test for Enrichment
plotSmear
Plots log-Fold Change versus log-Concentration (or, M versus A) for Count Data
plotMD.DGEList
Mean-Difference Plot of Count Data
zscoreNBinom
Z-score Equivalents of Negative Binomial Deviate
topTags
Table of the Top Differentially Expressed Tags
dispCoxReid
Estimate Common Dispersion for Negative Binomial GLMs
goana.DGELRT
Gene Ontology or KEGG Analysis of Differentially Expressed Genes
estimateExonGenewiseDisp
Estimate Genewise Dispersions from Exon-Level Count Data
estimateGLMTrendedDisp
Estimate Trended Dispersion for Negative Binomial GLMs
estimateGLMRobustDisp
Empirical Robust Bayes Tagwise Dispersions for Negative Binomial GLMs using Observation Weights
estimateTrendedDisp
Estimate Empirical Bayes Trended Dispersion Values
maximizeQuadratic
Maximize a function given a table of values by quadratic interpolation.
DGEGLM-class
Digital Gene Expression Generalized Linear Model results - class
commonCondLogLikDerDelta
Conditional Log-Likelihoods in Terms of Delta
sumTechReps
Sum Over Replicate Samples
subsetting
Subset DGEList, DGEGLM, DGEExact and DGELRT Objects
spliceVariants
Identify Genes with Splice Variants
thinCounts
Binomial or Multinomial Thinning of Counts
glmQLFit
Genewise Negative Binomial Generalized Linear Models with Quasi-likelihood Tests
equalizeLibSizes
Equalize Library Sizes by Quantile-to-Quantile Normalization
dglmStdResid
Visualize the mean-variance relationship in DGE data using standardized residuals
DGEList-class
Digital Gene Expression data - class
condLogLikDerSize
Conditional Log-Likelihood of the Dispersion for a Single Group of Replicate Libraries
estimateDisp
Estimate Common, Trended and Tagwise Negative Binomial dispersions by weighted likelihood empirical Bayes
adjustedProfileLik
Adjusted Profile Likelihood for the Negative Binomial Dispersion Parameter
cpm
Counts per Million or Reads per Kilobase per Million
estimateCommonDisp
Estimate Common Negative Binomial Dispersion by Conditional Maximum Likelihood
cutWithMinN
Cut numeric vector into non-empty intervals
as.data.frame
Turn a TopTags Object into a Dataframe
as.matrix
Turn a DGEList Object into a Matrix
DGEList
DGEList Constructor
camera.DGEList
Competitive Gene Set Test for Digital Gene Expression Data Accounting for Inter-gene Correlation
getCounts
Extract Specified Component of a DGEList Object
dimnames
Retrieve the Dimension Names of a DGE Object
getPriorN
Get a Recommended Value for Prior N from DGEList Object
glmTreat
Test for Differential Expression Relative to a Threshold
mglm
Fit Negative Binomial Generalized Linear Model to Multiple Response Vectors: Low Level Functions
validDGEList
Check for Valid DGEList object
exactTest
Exact Tests for Differences between Two Groups of Negative-Binomial Counts
maximizeInterpolant
Maximize a function given a table of values by spline interpolation.
systematicSubset
Take a systematic subset of indices.
q2qnbinom
Quantile to Quantile Mapping between Negative-Binomial Distributions
readDGE
Read and Merge a Set of Files Containing Count Data
maPlot
Plots Log-Fold Change versus Log-Concentration (or, M versus A) for Count Data
plotBCV
Plot Biological Coefficient of Variation
roast.DGEList
Rotation Gene Set Tests for Digital Gene Expression Data
romer.DGEList
Rotation Gene Set Tests for Digital Gene Expression Data
plotQLDisp
Plot the quasi-likelihood dispersion
dispBinTrend
Estimate Dispersion Trend by Binning for NB GLMs
edgeRUsersGuide
View edgeR User's Guide