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 |
buildDESeq |
buildDESeq - create CountDataSet |
buildDGEList |
buildDGEList - create DGEList (edgeR) |
combineND |
averageND, sumND, combineNS, log2ND - operations on distributions |
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 |
findRegionsAsND |
findRegionsAsND - finding regions of high coverage using Lindell-Aumann |
gcoverage |
regionCoverage |
geneInChromosome |
geneInChromosome |
getCoverageFromRS |
getCoverageFromRS - conversion to coverage object |
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 |
log2ND |
averageND, sumND, combineNS, log2ND - operations on distributions |
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 |
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 |
readsInRange |
readsInRange |
regionBasedCoverage |
regionBasedCoverage - transformation of the region coverage by the |
regionCoverage |
regionCoverage |
regionmining |
findRegionsAsND - finding regions of high coverage using Lindell-Aumann |
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 |
setSpecies |
setSpecies |
spaceInChromosome |
spaceInChromosome |
splicingind |
getSIFromND - calculating splicing index of two coverages |
sumND |
averageND, sumND, combineNS, log2ND - operations on distributions |
xmapConnected |
xmapConnected |