H3K27Ac                 ChIP-seq Samples for H3K27Ac in Human
                        Lymphoblastoid Cell Lines
MA.pcc                  Deduce Pearson Correlation Coefficient between
                        M & A Values
MAnorm2                 MAnorm2: a Package for Normalizing and
                        Comparing ChIP-seq Samples
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' Objects
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 'bioCond'
estParamHyperChIP       The Parameter Estimation Framework of HyperChIP
estimateD0              Workhorse Function for Estimating Number of
                        Prior Degrees of Freedom
estimateD0Robust        Estimate Number of Prior Degrees of Freedom in
                        a Robust Manner
estimatePriorDf         Assess the Goodness of Fit of Mean-Variance
                        Curves
estimatePriorDfRobust   Assess the Goodness of Fit of Mean-Variance
                        Curves in a Robust Manner
estimateSizeFactors     Estimate Size Factors of ChIP-seq Samples
estimateVarRatio        Estimate Relative Variance Ratio Factors of
                        'bioCond' Objects
extendMeanVarCurve      Extend the Application Scope of a Mean-Variance
                        Curve
fitMeanVarCurve         Fit a Mean-Variance Curve
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?
meanVarLocalFit         Fit Mean-Variance Trend by Local Regression
meanVarParaFit          Parametrically Fit a Mean-Variance Curve
mean_var_logwinf        Expectation and Variance of Log Winsorized _F_
                        Distribution
mvcID.new               Create a New Unique ID for a Mean-Variance
                        Curve
normBioCond             Perform MA Normalization on a Set of 'bioCond'
                        Objects
normBioCondBySizeFactors
                        Normalize 'bioCond' Objects by Their Size
                        Factors
normCoef                Deduce MA Normalization Coefficients
normalize               Perform MA Normalization on a Set of ChIP-seq
                        Samples
normalizeBySizeFactors
                        Normalize ChIP-seq Samples by Their Size
                        Factors
plot.aovBioCond         Plot an 'aovBioCond' Object
plot.matrix             Visualize a Matrix of Numeric Values
plot.varTestBioCond     Plot a 'varTestBioCond' Object
plotMVC                 Plot a Mean-Variance Curve on a Single
                        'bioCond' Object
plotMeanVarCurve        Plot a Mean-Variance Curve
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 Curves
setPriorDfRobust        The Robust Counterpart of 'setPriorDf'
setPriorDfVarRatio      Set the Number of Prior Degrees of Freedom and
                        Variance Ratio Factors
setWeight               Set the Weights of Signal Intensities Contained
                        in a 'bioCond'
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'
