bcbioRnaseq: Bcbio RNA-Seq

#' @export
#' @name as.DESeqDataSet
#' @rdname coerce
#' @usage as.DESeqDataSet(x, ...)
NULL

#' @export
#' @name as.DESeqTransform
#' @rdname coerce
#' @usage as.DESeqTransform(x, ...)
NULL

#' @export
#' @name as.DGEList
#' @rdname coerce
#' @usage as.DGEList(x, ...)
NULL

#' @aliases counts<-
#' @export counts counts<-
#' @name counts
#' @rdname counts
#' @usage
#' counts(object, ...)
#' counts(object, ...) <- value
NULL

#' @export
#' @name plot5Prime3PrimeBias
#' @rdname plot5Prime3PrimeBias
#' @usage plot5Prime3PrimeBias(object, ...)
NULL

#' @export
#' @name plotCorrelationHeatmap
#' @rdname plotCorrelationHeatmap
#' @usage plotCorrelationHeatmap(object, ...)
NULL

#' @export
#' @name plotCounts
#' @rdname plotCounts
#' @usage plotCounts(object, ...)
NULL

#' @export
#' @name plotCountsPerBiotype
#' @rdname plotCountsPerBiotype
#' @usage plotCountsPerBiotype(object, ...)
NULL

#' @export
#' @name plotCountsPerBroadClass
#' @rdname plotCountsPerBiotype
#' @usage plotCountsPerBroadClass(object, ...)
NULL

#' @export
#' @name plotCountsPerFeature
#' @rdname plotCountsPerFeature
#' @usage plotCountsPerFeature(object, ...)
NULL

#' @export
#' @name plotDegHeatmap
#' @rdname deprecated
#' @usage plotDegHeatmap(object, ...)
NULL

#' @export
#' @name plotDispEsts
#' @rdname plotDispEsts
#' @usage plotDispEsts(object, ...)
NULL

#' @export
#' @name plotExonicMappingRate
#' @rdname plotExonicMappingRate
#' @usage plotExonicMappingRate(object, ...)
NULL

#' @export
#' @name plotFeatureSaturation
#' @rdname plotFeatureSaturation
#' @usage plotFeatureSaturation(object, ...)
NULL

#' @export
#' @name plotGenderMarkers
#' @rdname plotGenderMarkers
#' @usage plotGenderMarkers(object, ...)
NULL

#' @export
#' @name plotIntronicMappingRate
#' @rdname plotIntronicMappingRate
#' @usage plotIntronicMappingRate(object, ...)
NULL

#' @export
#' @name plotMappedReads
#' @rdname plotMappedReads
#' @usage plotMappedReads(object, ...)
NULL

#' @export
#' @name plotMappingRate
#' @rdname plotMappingRate
#' @usage plotMappingRate(object, ...)
NULL

#' @export
#' @name plotMeanSd
#' @rdname plotMeanSd
#' @usage plotMeanSd(object, ...)
NULL

#' @export
#' @name plotPca
#' @rdname plotPca
#' @usage plotPca(object, ...)
NULL

#' @export
#' @name plotPcaCovariates
#' @rdname plotPcaCovariates
#' @usage plotPcaCovariates(object, ...)
NULL

#' @export
#' @name plotPseudoVsAlignedCounts
#' @rdname plotPseudoVsAlignedCounts
#' @usage plotPseudoVsAlignedCounts(object, ...)
NULL

#' @export
#' @name plotQc
#' @rdname plotQc
#' @usage plotQc(object, ...)
NULL

#' @export
#' @name plotRrnaMappingRate
#' @rdname plotRrnaMappingRate
#' @usage plotRrnaMappingRate(object, ...)
NULL

#' @export
#' @name plotTotalReads
#' @rdname plotTotalReads
#' @usage plotTotalReads(object, ...)
NULL

#' @export
#' @name relativeLogExpression
#' @rdname relativeLogExpression
#' @usage relativeLogExpression(object, ...)
NULL

#' @export
#' @name show
#' @rdname show
#' @usage show(object)
NULL

#' @export
#' @name slotAlignedCounts
#' @rdname slotAlignedCounts
#' @usage slotAlignedCounts(object, ...)
NULL

#' @export
#' @name tmm
#' @rdname tmm
#' @usage tmm(object, ...)
NULL

#' @export
#' @name updateObject
#' @rdname updateObject
#' @usage updateObject(object, ..., verbose = FALSE)
NULL