Man pages for Bioconductor-mirror/casper
Characterization of Alternative Splicing based on Paired-End Reads

annotatedGenome-classClass "annotatedGenome"
asymmetryCheckPlot asymmetry coefficients for the observed data and compare...
calcDenovoEstimate expression of gene splicing variants de novo.
calcExpEstimate expression of a known set of gene splicing variants.
denovoExprEstimate expression for de novo splicing variants.
denovoGeneExpr-classClass "denovoGenomeExpr"
denovoGenomeExpr-classClass "denovoGeneExpr"
distrsGSE37704Estimated read start and insert size distributions from MiSeq...
genePlotPlot exon structure for each transcript of a given gene.
getDistrsCompute fragment start and fragment length distributions
getIslandgetIsland returns the island id associated to a given entrez...
getNreadsGet total number of paths in each island from a pathCounts...
getReadsgetReads returns the reads stored in a 'procBam' object.
getRocOperating characteristics of differential expression analysis
hg19DBSubset of human genome (UCSC hg19 version)
K562.r1l1Toy RNA-seq data from RGASP project.
mergeBatchesMerge two ExpressionSet objects by doing quantile...
mergeExpMerge splicing variant expression from multiple samples
modelPriorSet prior distribution on expressed splicing variants.
modelPriorAS-classClass "modelPriorAS"
pathCountsCompute exon path counts
pathCounts-classClass "pathCounts"
plotExprPlot inferred gene structure and expression.
plot-methodsPlot estimated read start and fragment length distributions.
plotPriorASPlot prior distribution on set of expressed variants (i.e....
probNonEquiv'probNonEquiv' performs a Bayesian hypothesis test for...
procBamProcess BAM object
procBam-classClass "procBam"
procGenomeCreate an annotatedGenome object that stores information...
qqnormGenomeWideGenome-wide qq-normal and qq-gamma plots
quantileNormApply quantile normalization
relexprByGeneCompute relative expressions within each gene
rmShortInsertsRemove reads with short insert sizes from imported BAM files.
simMAESimulate Mean Absolute Error (MAE) in estimating isoform...
simMAEcheckModel checking for One Sample Problems.
simMultSamplesSimulate paired end reads for multiple future samples based...
simReadsFunction to simulate paired end reads following given read...
simulatedSamples-classClass "simulatedSamples"
splitGenomeByLengthSplit an annotatedGenome object into subsets according to...
subsetGenomesubsetGenome subsets an object of class annotatedGenome for a...
transcriptsExtracts transcript information (exon start and ends) from an...
txLength-methods~~ Methods for Function 'txLength' in Package 'casper' ~~
wrapDenovoRun all necessary steps to get expression estimates from...
wrapKnownRun all necessary steps to get expression estimates from...
Bioconductor-mirror/casper documentation built on June 1, 2017, 5:26 a.m.