Drop Levels of a Factor that Never Occur
Calculate Weighted Likelihood Empirical Bayes Estimates
Empirical Bayes Tagwise Dispersions for Negative Binomial GLMs
Gini dispersion index
Goodness of Fit Tests for Multiple GLM Fits
Estimate Dispersion Trend for Negative Binomial GLMs
Negative Binomial Deviance
Digital Gene Expression Likelihood Ratio Test data and results - class
differential expression of Digital Gene Expression data - class
Calculate Normalization Factors to Align Columns of a Count Matrix
Predictive log-fold changes
Empirical analysis of digital gene expression data in R
Average Log Counts Per Million
Multiple Testing Across Genes and Contrasts
Locally Weighted Mean By Column
Create a Plot of Exon Usage from Exon-Level Count Data
Retrieve the Dimensions of a DGEList, DGEExact, DGEGLM, DGELRT or TopTags Object
Differential splicing plot
Process raw data from pooled genetic sequencing screens
dispCoxReidInterpolateTagwise
Estimate Genewise Dispersion for Negative Binomial GLMs by Cox-Reid Adjusted Profile Likelihood
Exact Binomial Tests for Comparing Two Digital Libraries
Moving Average Smoother of Matrix Columns
expandAsMatrix
Split the Counts or Pseudocounts from a DGEList Object According To Group
Estimate Common Dispersion for Negative Binomial GLMs
weightedCondLogLikDerDelta
Weighted Conditional Log-Likelihood in Terms of Delta
Top table of differentially spliced genes or exons
Estimate Empirical Bayes Tagwise Dispersion Values
Multidimensional scaling plot of distances between digital gene expression profiles
Test for Differential Exon Usage
Explore the mean-variance relationship for DGE data
Genewise Negative Binomial Generalized Linear Models
Good-Turing Frequency Estimation
Normalize ChIP-Seq Read Counts to Input and Test for Enrichment
Plots log-Fold Change versus log-Concentration (or, M versus A) for Count Data
Mean-Difference Plot of Count Data
Z-score Equivalents of Negative Binomial Deviate
Table of the Top Differentially Expressed Tags
Estimate Common Dispersion for Negative Binomial GLMs
Gene Ontology or KEGG Analysis of Differentially Expressed Genes
Estimate Genewise Dispersions from Exon-Level Count Data
Estimate Trended Dispersion for Negative Binomial GLMs
Empirical Robust Bayes Tagwise Dispersions for Negative Binomial GLMs using Observation Weights
Estimate Empirical Bayes Trended Dispersion Values
Maximize a function given a table of values by quadratic interpolation.
Digital Gene Expression Generalized Linear Model results - class
Conditional Log-Likelihoods in Terms of Delta
Sum Over Replicate Samples
Subset DGEList, DGEGLM, DGEExact and DGELRT Objects
Identify Genes with Splice Variants
Binomial or Multinomial Thinning of Counts
Genewise Negative Binomial Generalized Linear Models with Quasi-likelihood Tests
Equalize Library Sizes by Quantile-to-Quantile Normalization
Visualize the mean-variance relationship in DGE data using standardized residuals
Digital Gene Expression data - class
Conditional Log-Likelihood of the Dispersion for a Single Group of Replicate Libraries
Estimate Common, Trended and Tagwise Negative Binomial dispersions by weighted likelihood empirical Bayes
Adjusted Profile Likelihood for the Negative Binomial Dispersion Parameter
Counts per Million or Reads per Kilobase per Million
Estimate Common Negative Binomial Dispersion by Conditional Maximum Likelihood
Cut numeric vector into non-empty intervals
Turn a TopTags Object into a Dataframe
Turn a DGEList Object into a Matrix
DGEList Constructor
Competitive Gene Set Test for Digital Gene Expression Data Accounting for Inter-gene Correlation
Extract Specified Component of a DGEList Object
Retrieve the Dimension Names of a DGE Object
Get a Recommended Value for Prior N from DGEList Object
Test for Differential Expression Relative to a Threshold
Fit Negative Binomial Generalized Linear Model to Multiple Response Vectors: Low Level Functions
Check for Valid DGEList object
Exact Tests for Differences between Two Groups of Negative-Binomial Counts
Maximize a function given a table of values by spline interpolation.
Take a systematic subset of indices.
Quantile to Quantile Mapping between Negative-Binomial Distributions
Read and Merge a Set of Files Containing Count Data
Plots Log-Fold Change versus Log-Concentration (or, M versus A) for Count Data
Plot Biological Coefficient of Variation
Rotation Gene Set Tests for Digital Gene Expression Data
Rotation Gene Set Tests for Digital Gene Expression Data
Plot the quasi-likelihood dispersion
Estimate Dispersion Trend by Binning for NB GLMs
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