calcNormFactors |
Calculate Normalization Factors to Align Columns of a Count Matrix |
calcNormFactors.default |
Calculate Normalization Factors to Align Columns of a Count Matrix |
calcNormFactors.DGEList |
Calculate Normalization Factors to Align Columns of a Count Matrix |
calcNormOffsetsforChIP |
Normalize ChIP-Seq Read Counts to Input and Test for Enrichment |
camera.DGEList |
Competitive Gene Set Test for Digital Gene Expression Data Accounting for Inter-gene Correlation |
commonCondLogLikDerDelta |
Conditional Log-Likelihoods in Terms of Delta |
condLogLikDerDelta |
Conditional Log-Likelihood of the Dispersion for a Single Group of Replicate Libraries |
condLogLikDerSize |
Conditional Log-Likelihood of the Dispersion for a Single Group of Replicate Libraries |
cpm |
Counts per Million or Reads per Kilobase per Million |
cpm.default |
Counts per Million or Reads per Kilobase per Million |
cpm.DGEList |
Counts per Million or Reads per Kilobase per Million |
cutWithMinN |
Cut numeric vector into non-empty intervals |
decideTestsDGE |
Multiple Testing Across Genes and Contrasts |
designAsFactor |
Fit Negative Binomial Generalized Linear Model to Multiple Response Vectors: Low Level Functions |
DGEExact-class |
differential expression of Digital Gene Expression data - class |
DGEGLM-class |
Digital Gene Expression Generalized Linear Model results - class |
DGEList |
DGEList Constructor |
DGEList-class |
Digital Gene Expression data - class |
DGELRT-class |
Digital Gene Expression Likelihood Ratio Test data and results - class |
dglmStdResid |
Visualize the mean-variance relationship in DGE data using standardized residuals |
diffSpliceDGE |
Test for Differential Exon Usage |
dim.DGEExact |
Retrieve the Dimensions of a DGEList, DGEExact, DGEGLM, DGELRT or TopTags Object |
dim.DGEGLM |
Retrieve the Dimensions of a DGEList, DGEExact, DGEGLM, DGELRT or TopTags Object |
dim.DGEList |
Retrieve the Dimensions of a DGEList, DGEExact, DGEGLM, DGELRT or TopTags Object |
dim.DGELRT |
Retrieve the Dimensions of a DGEList, DGEExact, DGEGLM, DGELRT or TopTags Object |
dim.TopTags |
Retrieve the Dimensions of a DGEList, DGEExact, DGEGLM, DGELRT or TopTags Object |
dimnames.DGEExact |
Retrieve the Dimension Names of a DGE Object |
dimnames.DGEGLM |
Retrieve the Dimension Names of a DGE Object |
dimnames.DGEList |
Retrieve the Dimension Names of a DGE Object |
dimnames.DGELRT |
Retrieve the Dimension Names of a DGE Object |
dimnames.TopTags |
Retrieve the Dimension Names of a DGE Object |
dimnames<-.DGEGLM |
Retrieve the Dimension Names of a DGE Object |
dimnames<-.DGEList |
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 Tagwise Dispersion for Negative Binomial GLMs by Cox-Reid Adjusted Profile Likelihood |
dispCoxReidPowerTrend |
Estimate Dispersion Trend for Negative Binomial GLMs |
dispCoxReidSplineTrend |
Estimate Dispersion Trend for Negative Binomial GLMs |
dispDeviance |
Estimate Common Dispersion for Negative Binomial GLMs |
dispPearson |
Estimate Common Dispersion for Negative Binomial GLMs |
getCounts |
Extract Specified Component of a DGEList Object |
getDispersion |
Extract Specified Component of a DGEList Object |
getDispersions |
Visualize the mean-variance relationship in DGE data using standardized residuals |
getOffset |
Extract Specified Component of a DGEList Object |
getPriorN |
Get a Recommended Value for Prior N from DGEList Object |
glmFit |
Genewise Negative Binomial Generalized Linear Models |
glmFit.default |
Genewise Negative Binomial Generalized Linear Models |
glmFit.DGEList |
Genewise Negative Binomial Generalized Linear Models |
glmLRT |
Genewise Negative Binomial Generalized Linear Models |
glmQLFit |
Quasi-likelihood methods with empirical Bayes shrinkage |
glmQLFTest |
Quasi-likelihood methods with empirical Bayes shrinkage |
goana.DGEExact |
Gene Ontology Analysis of Differentially Expressed Genes |
goana.DGELRT |
Gene Ontology Analysis of Differentially Expressed Genes |
gof |
Goodness of Fit Tests for Multiple GLM Fits |
goodTuring |
Good-Turing Frequency Estimation |
goodTuringPlot |
Good-Turing Frequency Estimation |
goodTuringProportions |
Good-Turing Frequency Estimation |
length.DGEExact |
Retrieve the Dimensions of a DGEList, DGEExact, DGEGLM, DGELRT or TopTags Object |
length.DGEGLM |
Retrieve the Dimensions of a DGEList, DGEExact, DGEGLM, DGELRT or TopTags Object |
length.DGEList |
Retrieve the Dimensions of a DGEList, DGEExact, DGEGLM, DGELRT or TopTags Object |
length.DGELRT |
Retrieve the Dimensions of a DGEList, DGEExact, DGEGLM, DGELRT or TopTags Object |
length.TopTags |
Retrieve the Dimensions of a DGEList, DGEExact, DGEGLM, DGELRT or TopTags Object |
locfitByCol |
Locally Weighted Mean By Column |
loessByCol |
Locally Weighted Mean By Column |
maPlot |
Plots Log-Fold Change versus Log-Concentration (or, M versus A) for Count Data |
maximizeInterpolant |
Maximize a function given a table of values by spline interpolation. |
maximizeQuadratic |
Maximize a function given a table of values by quadratic interpolation. |
mglm |
Fit Negative Binomial Generalized Linear Model to Multiple Response Vectors: Low Level Functions |
mglmLevenberg |
Fit Negative Binomial Generalized Linear Model to Multiple Response Vectors: Low Level Functions |
mglmOneGroup |
Fit Negative Binomial Generalized Linear Model to Multiple Response Vectors: Low Level Functions |
mglmOneWay |
Fit Negative Binomial Generalized Linear Model to Multiple Response Vectors: Low Level Functions |
movingAverageByCol |
Moving Average Smoother of Matrix Columns |
mroast.DGEList |
Rotation Gene Set Tests for Digital Gene Expression Data |
plotBCV |
Plot Biological Coefficient of Variation |
plotExonUsage |
Create a Plot of Exon Usage from Exon-Level Count Data |
plotMDS.DGEList |
Multidimensional scaling plot of distances between digital gene expression profiles |
plotMeanVar |
Explore the mean-variance relationship for DGE data |
plotQLDisp |
Plot the quasi-likelihood dispersion |
plotSmear |
Plots log-Fold Change versus log-Concentration (or, M versus A) for Count Data |
plotSpliceDGE |
Plot exons on differentially spliced gene |
predFC |
Predictive log-fold changes |
predFC.default |
Predictive log-fold changes |
predFC.DGEList |
Predictive log-fold changes |
processAmplicons |
Process raw data from pooled genetic sequencing screens |