edgeR v3.14.0

by Yunshun Chen

Empirical Analysis of Digital Gene Expression Data in R

Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE.

Functions in edgeR

Name Description
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
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Details

Date 2016-04-19
License GPL (>=2)
URL http://bioinf.wehi.edu.au/edgeR
biocViews GeneExpression, Transcription, AlternativeSplicing, Coverage, DifferentialExpression, DifferentialSplicing, GeneSetEnrichment, Genetics, Bayesian, Clustering, Regression, TimeCourse, SAGE, Sequencing, ChIPSeq, RNASeq, BatchEffect, MultipleComparison, Normalization, QualityControl

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