Man pages for rnaSeqMap
rnaSeq secondary analyses

addBamDataaddBamData - getting sample data from BAM file.
addDataToReadsetaddDataToReadset - adding one more sample in the SeqRead on R...
addExperimentsToReadsetaddExperimentsToReadset - getting sample data from the...
averageNDaverageND, sumND, combineNS, log2ND - operations on...
bam2sigbam2sig - encapsulated pipeline of finding significant...
buildDESeqbuildDESeq - create CountDataSet
buildDGEListbuildDGEList - create DGEList (edgeR)
findRegionsAsIRfindRegionsAsIR - finding regions of high coverage using...
findRegionsAsNDfindRegionsAsND - finding regions of high coverage using...
fiveCol2GRangesfiveCol2GRanges
geneInChromosomegeneInChromosome
generatorsGenerators for synt data and
getBamDatagetBamData - getting sample data from BAM file.
getCoverageFromRSgetCoverageFromRS - conversion to coverage object
getDataData accessor function for rnaSeqMap objects containing...
getExpDescriptiongetExpDescription
getFCFromNDgetFCFromND - calculating fold change of coverages
getSIFromNDgetSIFromND - calculating splicing index of two coverages
getSumsExpgetSumsExp
gRanges2CamelMeasuresGenomic plots based upon NucleotideDistr objects
measuresMeasures
NDplotsGenomic plots based upon NucleotideDistr objects
normalizationsNormalization Methods
normalizeBySumNormalization of NucleotideDistr by global number of reads
NucleotideDistr-classNumeric distributions by nucleotide - class
parseGff3parseGff3 - parsing gff3 file format
plotGeneCoverageGenomic plots with rnaSeqMap
readsInRangereadsInRange
regionBasedCoverageregionBasedCoverage - transformation of the region coverage...
regionCoverageregionCoverage
RleList2matrixRleList2matrix
rs.listExample of sequencing data for rnaSeqMap library
SeqRedsSeqReads - a container for RNAseq reads
setDataData accessor function for rnaSeqMap objects containing...
setSAXPYDataData accessor function for rnaSeqMap objects containing...
setSpeciessetSpecies
simplePlotsimplePlot - quick plot for the coverages
spaceInChromosomespaceInChromosome
rnaSeqMap documentation built on Nov. 17, 2017, 10:36 a.m.