Empirical Analysis of Digital Gene Expression Data in R

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 | Calculate Normalization Factors to Align Columns of a Count... |

camera.DGEList | Competitive Gene Set Test for Digital Gene Expression Data... |

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 | Visualize the 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 |

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 |

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 |

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 Model to Multiple... |

movingAverageByCol | Moving Average Smoother of Matrix Columns |

nbinomDeviance | Negative Binomial Deviance |

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 data from pooled genetic sequencing screens |

q2qnbinom | Quantile to Quantile Mapping between Negative-Binomial... |

readDGE | Read and Merge a Set of Files Containing Count Data |

roast.DGEList | Rotation Gene Set Tests for Digital Gene Expression Data |

romer.DGEList | Rotation Gene Set Tests for Digital Gene Expression Data |

scaleOffset | Scale offsets |

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 Tags |

validDGEList | Check for Valid DGEList object |

weightedCondLogLikDerDelta | Weighted Conditional Log-Likelihood in Terms of Delta |

WLEB | Calculate Weighted Likelihood Empirical Bayes Estimates |

zscoreNBinom | Z-score Equivalents of Negative Binomial Deviate |

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