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| 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. |
| allCamelMeasuresForRegion | Genomic plots based upon NucleotideDistr objects |
| 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) |
| combineND | averageND, sumND, combineNS, log2ND - operations on distributions |
| densityNormalize | Normalization Methods |
| diff_area | Measures |
| diff_derivative_area | Measures |
| distrCOVPlot | Genomic plots based upon NucleotideDistr objects |
| distrCOVPlotg | Genomic plots based upon NucleotideDistr objects |
| distribs | Numeric distributions by nucleotide - class |
| distrSIPlot | 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 |
| gcoverage | regionCoverage |
| geneInChromosome | geneInChromosome |
| generatorAdd | Generators for synt data and |
| generatorAddSquare | Generators for synt data and |
| generatorMultiply | Generators for synt data and |
| generatorPeak | Generators for synt data and |
| generatorSynth | Generators for synt data and |
| generatorTrunc | 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 |
| getDistr | Numeric distributions by nucleotide - class |
| getExpDescription | getExpDescription |
| getFCFromND | getFCFromND - calculating fold change of coverages |
| getSIFromND | getSIFromND - calculating splicing index of two coverages |
| getSumsExp | getSumsExp |
| ghistogram | Genomic plots with rnaSeqMap |
| globalCountsNormalize | Normalization Methods |
| gRanges2CamelMeasures | Genomic plots based upon NucleotideDistr objects |
| hump_diff1 | Measures |
| hump_diff2 | Measures |
| ks_test | Measures |
| log2ND | averageND, sumND, combineNS, log2ND - operations on distributions |
| min_maxNormalize | Normalization Methods |
| newNuctleotideDistr | Numeric distributions by nucleotide - class |
| newSeqReads | SeqReads - a container for RNAseq reads |
| newSeqReadsFromGene | SeqReads - a container for RNAseq reads |
| normalizeBySum | Normalization of NucleotideDistr by global number of reads |
| NucleotideDistr-class | Numeric distributions by nucleotide - class |
| parseGff3 | parseGff3 - parsing gff3 file format |
| plotCoverageHistogram | Genomic plots with rnaSeqMap |
| plotExonCoverage | Genomic plots with rnaSeqMap |
| plotGeneCoverage | Genomic plots with rnaSeqMap |
| plotGeneExonCoverage | Genomic plots with rnaSeqMap |
| plotRegionCoverage | Genomic plots with rnaSeqMap |
| plotSI | Genomic plots with rnaSeqMap |
| pp_derivative_plot | Measures |
| pp_plot | Measures |
| qq_derivative_plot | Measures |
| qq_plot | Measures |
| readsInRange | readsInRange |
| regionBasedCoverage | regionBasedCoverage - transformation of the region coverage by the Lindell-Aumann regions |
| regionCoverage | regionCoverage |
| regionmining | findRegionsAsND - finding regions of high coverage using Lindell-Aumann algorithm. |
| RleList2matrix | RleList2matrix |
| rs.list | Example of sequencing data for rnaSeqMap library |
| sample_data_rnaSeqMap | Example of sequencing data for rnaSeqMap library |
| SeqReads | SeqReads - a container for RNAseq reads |
| SeqReads-class | SeqReads - a container for RNAseq reads |
| 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 |
| splicingind | getSIFromND - calculating splicing index of two coverages |
| standarizationNormalize | Normalization Methods |
| sumND | averageND, sumND, combineNS, log2ND - operations on distributions |