addPriorCount | Add a prior count |
adjustedProfileLik | Adjusted Profile Likelihood for the Negative Binomial... |
asdataframe | Turn a TopTags Object into a Dataframe |
asmatrix | Turn a DGEList Object into a Matrix |
aveLogCPM | Average Log Counts Per Million |
binomTest | Exact Binomial Tests for Comparing Two Digital Libraries |
calcNormFactors | Library Size Normalization |
camera.DGEList | Competitive Gene Set Tests for Digital Gene Expression Data |
catchSalmon | Process Kallisto or Salmon Output |
cbind | Combine DGEList Objects |
commonCondLogLikDerDelta | Conditional Log-Likelihoods in Terms of Delta |
condLogLikDerSize | Conditional Log-Likelihood of the Dispersion for a Single... |
cpm | Counts per Million or Reads per Kilobase per Million |
cutWithMinN | Cut numeric vector into non-empty intervals |
decidetestsDGE | Multiple Testing Across Genes and Contrasts |
DGEExact-class | differential expression of Digital Gene Expression data -... |
DGEGLM-class | Digital Gene Expression Generalized Linear Model results -... |
DGEList | DGEList Constructor |
DGEList-class | Digital Gene Expression data - class |
DGELRT-class | Digital Gene Expression Likelihood Ratio Test data and... |
dglmStdResid | Plot Mean-Variance Relationship in DGE Data Using... |
diffSpliceDGE | Test for Differential Exon Usage |
dim | Retrieve the Dimensions of a DGEList, DGEExact, DGEGLM,... |
dimnames | Retrieve the Dimension Names of a DGE Object |
dispBinTrend | Estimate Dispersion Trend by Binning for NB GLMs |
dispCoxReid | Estimate Common Dispersion for Negative Binomial GLMs |
dispCoxReidInterpolateTagwise | Estimate Genewise Dispersion for Negative Binomial GLMs by... |
dispCoxReidSplineTrend | Estimate Dispersion Trend for Negative Binomial GLMs |
dropEmptyLevels | Drop Levels of a Factor that Never Occur |
edgeR-package | Empirical analysis of digital gene expression data in R |
edgeRUsersGuide | View edgeR User's Guide |
effectiveLibSizes | Effective Library Sizes |
equalizeLibSizes | Equalize Library Sizes by Quantile-to-Quantile Normalization |
estimateCommonDisp | Estimate Common Negative Binomial Dispersion by Conditional... |
estimateDisp | Estimate Common, Trended and Tagwise Negative Binomial... |
estimateExonGenewisedisp | Estimate Genewise Dispersions from Exon-Level Count Data |
estimateGLMCommonDisp | Estimate Common Dispersion for Negative Binomial GLMs |
estimateGLMRobustDisp | Empirical Robust Bayes Tagwise Dispersions for Negative... |
estimateGLMTagwiseDisp | Empirical Bayes Tagwise Dispersions for Negative Binomial... |
estimateGLMTrendedDisp | Estimate Trended Dispersion for Negative Binomial GLMs |
estimateTagwiseDisp | Estimate Empirical Bayes Tagwise Dispersion Values |
estimateTrendedDisp | Estimate Empirical Bayes Trended Dispersion Values |
exactTest | Exact Tests for Differences between Two Groups of... |
expandAsMatrix | expandAsMatrix |
filterByExpr | Filter Genes By Expression Level |
getCounts | Extract Specified Component of a DGEList Object |
getPriorN | Get a Recommended Value for Prior N from DGEList Object |
gini | Gini dispersion index |
glmfit | Genewise Negative Binomial Generalized Linear Models |
glmQLFTest | Genewise Negative Binomial Generalized Linear Models with... |
glmTreat | Test for Differential Expression Relative to a Threshold |
goana | Gene Ontology or KEGG Analysis of Differentially Expressed... |
gof | Goodness of Fit Tests for Multiple GLM Fits |
goodTuring | Good-Turing Frequency Estimation |
head | Return the First to Last Part of a Data Object |
loessByCol | Locally Weighted Mean By Column |
makeCompressedMatrix | makeCompressedMatrix |
maPlot | Plots Log-Fold Change versus Log-Concentration (or, M versus... |
maximizeInterpolant | Maximize a function given a table of values by spline... |
maximizeQuadratic | Maximize a function given a table of values by quadratic... |
meanvar | Explore the Mean-Variance Relationship for DGE Data |
mglm | Fit Negative Binomial Generalized Linear Models to Multiple... |
modelMatrixMeth | Construct Design Matrix for edgeR Analysis of Methylation... |
movingAverageByCol | Moving Average Smoother of Matrix Columns |
nbinomDeviance | Negative Binomial Deviance |
nbinomUnitDeviance | Negative Binomial Unit Deviance |
nearestReftoX | Find Nearest Element of Reference for each Element of X |
nearestTSS | Find Nearest Transcriptional Start Site |
normalizeChIPtoInput | Normalize ChIP-Seq Read Counts to Input and Test for... |
plotBCV | Plot Biological Coefficient of Variation |
plotExonUsage | Create a Plot of Exon Usage from Exon-Level Count Data |
plotMD | Mean-Difference Plot of Count Data |
plotMDS.DGEList | Multidimensional scaling plot of distances between digital... |
plotQLDisp | Plot the quasi-likelihood dispersion |
plotSmear | Smear plot |
plotSpliceDGE | Differential splicing plot |
predFC | Predictive log-fold changes |
processAmplicons | Process raw fastq data from pooled genetic sequencing screens |
q2qnbinom | Quantile to Quantile Mapping between Negative-Binomial... |
read10X | Read 10X Genomics Files |
readBismark2DGE | Read Bismark Coverage Files |
readDGE | Read and Merge a Set of Files Containing Count Data |
roast.DGEList | Self-contained Gene Set Tests for Digital Gene Expression... |
romer.DGEList | Rotation Gene Set Enrichment for Digital Gene Expression Data |
rowsum | Sum Over Groups of Genes |
scaleOffset | Scale offsets |
SE2DGEList | SummarizedExperiment to DGEList |
spliceVariants | Identify Genes with Splice Variants |
splitIntoGroups | Split the Counts or Pseudocounts from a DGEList Object... |
subsetting | Subset DGEList, DGEGLM, DGEExact and DGELRT Objects |
sumTechReps | Sum Over Replicate Samples |
systematicSubset | Take a systematic subset of indices. |
thinCounts | Binomial or Multinomial Thinning of Counts |
topSpliceDGE | Top table of differentially spliced genes or exons |
topTags | Table of the Top Differentially Expressed Genes/Tags |
validDGEList | Check for Valid DGEList object |
voomLmFit | Apply voom-lmFit Pipeline While Accounting for Loss of... |
weightedCondLogLikDerDelta | Weighted Conditional Log-Likelihood in Terms of Delta |
WLEB | Weighted Likelihood Empirical Bayes |
zscoreNBinom | Z-score Equivalents of Negative Binomial Deviate |
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