Class "CountDataSet" - a container for count data from HTS experiments
Adjust an SCV value for the bias arising when it is calculated from unbiased estimates of mean and variance.
Accessor functions for the 'conditions' information in a CountDataSet object.
Accessors for the 'counts' slot of a CountDataSet object.
Accessor function for the dispTable information in a CountDataSet
Estimate and fit dispersions for a CountDataSet.
Estimate the size factors for a CountDataSet
Low-level function to estimate size factors with robust regression.
REMOVED
Accessor function for the fitInfo objects in a CountDataSet
Fit a generalized linear model (GLM) for each gene.
Fit negative binomial GLMs to a count matrix.
Perform row-wise estimates of base-level means and variances for count data.
Apply a variance stabilizing transformation (VST) to the count data
make a simple example CountDataSet with random data
Perform chi-squared tests comparing two sets of GLM fits
Test for differences between the base means for two conditions
Perform row-wise tests for differences between the base means of two count matrices.
GLM family for a negative binomial with known dispersion and log link with size factors
Create a CountDataSet object
Create a new CountDataSet from count files generated with htseq-count
Plot dispersion estimates and fitted values
Makes a so-called "MA-plot"
Sample PCA plot from variance-stabilized data
REMOVED
REMOVED
Accessor functions for the 'sizeFactors' information in a CountDataSet object.
REMOVED