NucleotideDistr-class   Numeric distributions by nucleotide - class
RleList2matrix          RleList2matrix
SeqReads                SeqReads - a container for RNAseq reads
addBamData              addBamData - getting sample data from BAM file.
addDataToReadset        addDataToReadset - adding one more sample in
                        the SeqRead on R level
addExperimentsToReadset
                        addExperimentsToReadset - getting sample data
                        from the database.
averageND               averageND, sumND, combineNS, log2ND -
                        operations on distributions
bam2sig                 bam2sig - encapsulated pipeline of finding
                        significant expression
buildDESeq              buildDESeq - create CountDataSet
buildDGEList            buildDGEList - create DGEList (edgeR)
distrCOVPlot            Genomic plots based upon NucleotideDistr
                        objects
findRegionsAsIR         findRegionsAsIR - finding regions of high
                        coverage using Lindell-Aumann algorithm.
findRegionsAsND         findRegionsAsND - finding regions of high
                        coverage using Lindell-Aumann algorithm.
fiveCol2GRanges         fiveCol2GRanges
gRanges2CamelMeasures   Genomic plots based upon NucleotideDistr
                        objects
geneInChromosome        geneInChromosome
generatorAddSquare      Generators for synt data and
getBamData              getBamData - getting sample data from BAM file.
getCoverageFromRS       getCoverageFromRS - conversion to coverage
                        object
getData                 Data accessor function for rnaSeqMap objects
                        containing 'data' field
getExpDescription       getExpDescription
getFCFromND             getFCFromND - calculating fold change of
                        coverages
getSIFromND             getSIFromND - calculating splicing index of two
                        coverages
getSumsExp              getSumsExp
ks_test                 Measures
normalizeBySum          Normalization of NucleotideDistr by global
                        number of reads
parseGff3               parseGff3 - parsing gff3 file format
plotGeneCoverage        Genomic plots with rnaSeqMap
readsInRange            readsInRange
regionBasedCoverage     regionBasedCoverage - transformation of the
                        region coverage by the Lindell-Aumann regions
regionCoverage          regionCoverage
rs.list                 Example of sequencing data for rnaSeqMap
                        library
setData                 Data accessor function for rnaSeqMap objects
                        containing 'data' field
setSAXPYData            Data accessor function for rnaSeqMap objects
                        containing 'data' field
setSpecies              setSpecies
simplePlot              simplePlot - quick plot for the coverages
spaceInChromosome       spaceInChromosome
standarizationNormalize
                        Normalization Methods
