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
Digital Gene Expression data - class
DGEList Constructor
Calculate Weighted Likelihood Empirical Bayes Estimates
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
Calculate Normalization Factors to Align Columns of a Count Matrix
Competitive Gene Set Test for Digital Gene Expression Data Accounting for Inter-gene Correlation
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
Visualize the 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
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
Extract Specified Component of a DGEList Object
Get a Recommended Value for Prior N from DGEList Object
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
Locally Weighted Mean By Column
Plots Log-Fold Change versus Log-Concentration (or, M versus A) for Count Data
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 Model to Multiple Response Vectors: Low Level Functions
Moving Average Smoother of Matrix Columns
Negative Binomial Deviance
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
Plots log-Fold Change versus log-Concentration (or, M versus A) for Count Data
Differential splicing plot
Predictive log-fold changes
Process raw data from pooled genetic sequencing screens
Quantile to Quantile Mapping between Negative-Binomial Distributions
Read and Merge a Set of Files Containing Count Data
Rotation Gene Set Tests for Digital Gene Expression Data
Rotation Gene Set Tests for Digital Gene Expression Data
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 Tags
Check for Valid DGEList object
Weighted Conditional Log-Likelihood in Terms of Delta
Z-score Equivalents of Negative Binomial Deviate