aovBioCond | Perform a Moderated Analysis of Variance on 'bioCond' Objects |
bioCond | Create a 'bioCond' Object to Group ChIP-seq Samples |
checkCountTable | Check the Regularity of a Count Table |
checkIndex | Check the Validity of an Index Vector |
cmbBioCond | Combine a Set of 'bioCond' Objects into a Single 'bioCond' |
diffTest | Generic Differential Test |
distBioCond | Quantify the Distance between Each Pair of Samples in a... |
estimateD0 | Workhorse Function for Estimating Number of Prior Degrees of... |
estimateD0Robust | Estimate Number of Prior Degrees of Freedom in a Robust... |
estimatePriorDf | Assess the Goodness of Fit of Mean-Variance Curves |
estimatePriorDfRobust | Assess the Goodness of Fit of Mean-Variance Curves in a... |
estimateSizeFactors | Estimate Size Factors of ChIP-seq Samples |
estimateVarRatio | Estimate Relative Variance Ratio Factors of 'bioCond' Objects |
estParamHyperChIP | The Parameter Estimation Framework of HyperChIP |
extendMeanVarCurve | Extend the Application Scope of a Mean-Variance Curve |
fitMeanVarCurve | Fit a Mean-Variance Curve |
H3K27Ac | ChIP-seq Samples for H3K27Ac in Human Lymphoblastoid Cell... |
intervalMeans | Deduce the Sample Mean Signal Intensity |
intervalVars | Sample Variance of Replicated Signal Intensities |
inv.trigamma | Inversion of Trigamma Function |
isSymPosDef | Is a Real Matrix Symmetric and Positive Definite? |
MAnorm2 | MAnorm2: a Package for Normalizing and Comparing ChIP-seq... |
MA.pcc | Deduce Pearson Correlation Coefficient between M & A Values |
MAplot | Generic MA Plotting |
MAplot.bioCond | Create an MA Plot on Two 'bioCond' Objects |
MAplot.diffBioCond | Create an MA Plot on Results of Comparing Two 'bioCond'... |
meanVarLocalFit | Fit Mean-Variance Trend by Local Regression |
mean_var_logwinf | Expectation and Variance of Log Winsorized _F_ Distribution |
meanVarParaFit | Parametrically Fit a Mean-Variance Curve |
mvcID.new | Create a New Unique ID for a Mean-Variance Curve |
normalize | Perform MA Normalization on a Set of ChIP-seq Samples |
normalizeBySizeFactors | Normalize ChIP-seq Samples by Their Size Factors |
normBioCond | Perform MA Normalization on a Set of 'bioCond' Objects |
normBioCondBySizeFactors | Normalize 'bioCond' Objects by Their Size Factors |
normCoef | Deduce MA Normalization Coefficients |
plot.aovBioCond | Plot an 'aovBioCond' Object |
plot.matrix | Visualize a Matrix of Numeric Values |
plotMeanVarCurve | Plot a Mean-Variance Curve |
plotMVC | Plot a Mean-Variance Curve on a Single 'bioCond' Object |
plot.varTestBioCond | Plot a 'varTestBioCond' Object |
print.bioCond | Print a 'bioCond' Object |
print.summaryBioCond | Print a 'summaryBioCond' Object |
scaleMeanVarCurve | Scale a Mean-Variance Curve |
scaleMeanVarCurveRobust | Scale a Mean-Variance Curve in a Robust Manner |
setMeanVarCurve | Set the Mean-Variance Curve of a Set of 'bioCond' Objects |
setPriorDf | Set the Number of Prior Degrees of Freedom of Mean-Variance... |
setPriorDfRobust | The Robust Counterpart of 'setPriorDf' |
setPriorDfVarRatio | Set the Number of Prior Degrees of Freedom and Variance Ratio... |
setWeight | Set the Weights of Signal Intensities Contained in a... |
summary.bioCond | Summarize a 'bioCond' Object |
util.trigamma | Utility Trigamma Function |
varRatio | Compare Variance Ratio Factors of Two 'bioCond' Objects |
varTestBioCond | Call Hypervariable and Invariant Intervals for a 'bioCond' |
vstBioCond | Apply a Variance-Stabilizing Transformation to a 'bioCond' |
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