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
Seurat or SeuratObject class object to pseudo-bulk DGEList
Adjusted Profile Likelihood for the Negative Binomial Dispersion Parameter
Collapse TopTags or Other edgeR Object to a Data Frame
Collapse a DGEList or DGEGLM Object to a Matrix
Exact Binomial Tests for Comparing Two Digital Libraries
Competitive Gene Set Tests for Digital Gene Expression Data
Process Salmon, kallisto or RSEM Transcript Output
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
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
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
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
Convert featureCounts object to a DGEList
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-Dispersion Estimation
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
Return the First to Last Part of a Data Object
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 Models to Multiple Response Vectors: Low Level Functions
Construct Design Matrix for edgeR Analysis of Methylation Count Data
Moving Average Smoother of Matrix Columns
Find Nearest Element of Reference for each Element of X
Apply Microarray Normalization to DGEList
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
Multidimensional scaling plot of distances between digital gene expression profiles
Process FASTQ files from pooled genetic sequencing screens
Quantile to Quantile Mapping between Negative-Binomial Distributions
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
Split the Counts or Pseudocounts from a DGEList Object According To Group
Subset DGEList, DGEGLM, DGEExact and DGELRT Objects
Binomial or Multinomial Thinning of Counts
Top table of differentially spliced genes or exons
Table of the Top Differentially Expressed Genes/Tags
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