# 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 | |

No Results! |

## Last year downloads

## 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 |

depends | base (>= 2.15.0) , limma , R (>= 2.15.0) |

imports | graphics , methods , stats , utils |

suggests | KernSmooth , locfit , MASS , splines , statmod |

Contributors | Gordon Smyth, Aaron Lun, Yunshun Chen, Davis McCarthy, Xiaobei Zhou, Mark Robinson |

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