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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