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.
geneInChromosome        geneInChromosome
getBamData              getBamData - getting sample data from BAM file.
getCoverageFromRS       getCoverageFromRS - conversion to coverage
                        object
getExpDescription       getExpDescription
getFCFromND             getFCFromND - calculating fold change of
                        coverages
getSIFromND             getSIFromND - calculating splicing index of two
                        coverages
getSumsExp              getSumsExp
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
setSpecies              setSpecies
spaceInChromosome       spaceInChromosome
xmapConnected           xmapConnected
