CVTrainIndexGene        CV index matrix
expData                 expand the surrounding sequences
expData2nt              expand the surrounding sequences, including
                        both the single nucleotide and dinucleotide
                        composition
g1_part                 a part of g1.csv
getDev                  Poisson deviance
getNullCount            counts under null model
getOriLogPref           initialize for mart
getPredCount            predicted counts
getWeight               weight vector
glmPred                 predict using iterative glm
glmPred2nt              predict using iterative glm with dinucleotide
                        composition
iterGlm                 iterative generalized linear regression
iterGlm2nt              iterative generalized linear regression using
                        dinucleotide composition
iterGlmCV               cross-validation for iterative glm
iterGlmCV2nt            cross-validation for iterative glm using
                        dinucleotide composition
martCV                  cross-validation for MART
martPred                predict using MART
martTrain               train using MART
mseq-package            Modeling non-uniformity in short-read rates in
                        RNA-Seq data
plotCoef                plot coefficients of Poisson linear model
plotCounts              plot counts
setOriOffset            initialize
updateOffset            update offsets
