edgeR

differential expression of Digital Gene Expression data - class

Digital Gene Expression Generalized Linear Model results - class

Digital Gene Expression Likelihood Ratio Test data and results - class

DGEList Constructor

Digital Gene Expression data - class

SummarizedExperiment to DGEList

Weighted Likelihood Empirical Bayes

Add a prior count

Adjusted Profile Likelihood for the Negative Binomial Dispersion Parameter

Turn a TopTags Object into a Dataframe

Turn a DGEList Object into a Matrix

Average Log Counts Per Million

Exact Binomial Tests for Comparing Two Digital Libraries

Library Size Normalization

Competitive Gene Set Tests for Digital Gene Expression Data

Process Kallisto or Salmon Output

Combine DGEList Objects

Conditional Log-Likelihoods in Terms of Delta

Conditional Log-Likelihood of the Dispersion for a Single Group of Replicate Libraries

Counts per Million or Reads per Kilobase per Million

Cut numeric vector into non-empty intervals

Multiple Testing Across Genes and Contrasts

Plot Mean-Variance Relationship in DGE Data Using Standardized Residuals

Test for Differential Exon Usage

Retrieve the Dimensions of a DGEList, DGEExact, DGEGLM, DGELRT or TopTags Object

Retrieve the Dimension Names of a DGE Object

Estimate Dispersion Trend by Binning for NB GLMs

Estimate Common Dispersion for Negative Binomial GLMs

Estimate Genewise Dispersion for Negative Binomial GLMs by Cox-Reid Adjusted Profile Likelihood

Estimate Dispersion Trend for Negative Binomial GLMs

Drop Levels of a Factor that Never Occur

Empirical analysis of digital gene expression data in R

View edgeR User's Guide

Effective Library Sizes

Equalize Library Sizes by Quantile-to-Quantile Normalization

Estimate Common Negative Binomial Dispersion by Conditional Maximum Likelihood

Estimate Common, Trended and Tagwise Negative Binomial dispersions by weighted likelihood empirical Bayes

Estimate Genewise Dispersions from Exon-Level Count Data

Estimate Common Dispersion for Negative Binomial GLMs

Empirical Robust Bayes Tagwise Dispersions for Negative Binomial GLMs using Observation Weights

Empirical Bayes Tagwise Dispersions for Negative Binomial GLMs

Estimate Trended Dispersion for Negative Binomial GLMs

Estimate Empirical Bayes Tagwise Dispersion Values

Estimate Empirical Bayes Trended Dispersion Values

Exact Tests for Differences between Two Groups of Negative-Binomial Counts

expandAsMatrix

Filter Genes By Expression Level

Extract Specified Component of a DGEList Object

Get a Recommended Value for Prior N from DGEList Object

Gini dispersion index

Genewise Negative Binomial Generalized Linear Models with Quasi-likelihood Tests

Test for Differential Expression Relative to a Threshold

Genewise Negative Binomial Generalized Linear Models

Gene Ontology or KEGG Analysis of Differentially Expressed Genes

Goodness of Fit Tests for Multiple GLM Fits

Good-Turing Frequency Estimation

Return the First to Last Part of a Data Object

Locally Weighted Mean By Column

Plots Log-Fold Change versus Log-Concentration (or, M versus A) for Count Data

makeCompressedMatrix

Maximize a function given a table of values by spline interpolation.

Maximize a function given a table of values by quadratic interpolation.

Explore the Mean-Variance Relationship for DGE Data

Fit Negative Binomial Generalized Linear Models to Multiple Response Vectors: Low Level Functions

Construct Design Matrix for edgeR Analysis of Methylation Count Data

Moving Average Smoother of Matrix Columns

Negative Binomial Deviance

Negative Binomial Unit Deviance

Find Nearest Element of Reference for each Element of X

Find Nearest Transcriptional Start Site

Normalize ChIP-Seq Read Counts to Input and Test for Enrichment

Plot Biological Coefficient of Variation

Create a Plot of Exon Usage from Exon-Level Count Data

Mean-Difference Plot of Count Data

Multidimensional scaling plot of distances between digital gene expression profiles

Plot the quasi-likelihood dispersion

Smear plot

Differential splicing plot

Predictive log-fold changes

Process raw fastq data from pooled genetic sequencing screens

Quantile to Quantile Mapping between Negative-Binomial Distributions

Read 10X Genomics Files

Read Bismark Coverage Files

Read and Merge a Set of Files Containing Count Data

Self-contained Gene Set Tests for Digital Gene Expression Data

Rotation Gene Set Enrichment for Digital Gene Expression Data

Sum Over Groups of Genes

Scale offsets

Identify Genes with Splice Variants

Split the Counts or Pseudocounts from a DGEList Object According To Group

Subset DGEList, DGEGLM, DGEExact and DGELRT Objects

Sum Over Replicate Samples

Take a systematic subset of indices.

Binomial or Multinomial Thinning of Counts

Top table of differentially spliced genes or exons

Table of the Top Differentially Expressed Genes/Tags

Check for Valid DGEList object

Apply voom-lmFit Pipeline While Accounting for Loss of Residual DF Due to Exact Zeros

Weighted Conditional Log-Likelihood in Terms of Delta

Z-score Equivalents of Negative Binomial Deviate