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Last data update: 2014.03.03

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Results 1 - 10 of 17 found.
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EDASeq-package (Package: EDASeq) : Exploratory Data Analysis and Normalization for RNA-Seq data

Numerical summaries and graphical representations of some key features of the data along with implementations of both within-lane normalization methods for GC content bias and between-lane normalization methods to adjust for sequencing depth and possibly other differences in distribution.

● Data Source: BioConductor
● Keywords:
● Alias: EDASeq, EDASeq-package
● 0 images

MDPlot-methods (Package: EDASeq) : Methods for Function code{MDPlot

MDPlot produces a mean-difference smooth scatterplot of two lanes in an experiment.

● Data Source: BioConductor
● Keywords: methods
● Alias: MDPlot, MDPlot,SeqExpressionSet,numeric-method, MDPlot,matrix,numeric-method, MDPlot-methods
● 1 images

SeqExpressionSet-class (Package: EDASeq) : "SeqExpressionSet" class for collections of short reads

This class represents a collection of digital expression data (usually counts from RNA-Seq technology) along with sample information.

● Data Source: BioConductor
● Keywords: classes
● Alias: SeqExpressionSet-class, coerce,SeqExpressionSet,CountDataSet-method, counts,SeqExpressionSet-method, counts<-,SeqExpressionSet,ANY-method, exprs,SeqExpressionSet-method, exprs<-,SeqExpressionSet,ANY-method, initialize,SeqExpressionSet-method, normCounts, normCounts,SeqExpressionSet-method, normCounts<-, normCounts<-,SeqExpressionSet,ANY-method, normCounts<-,SeqExpressionSet-method, offst, offst,SeqExpressionSet-method, offst<-, offst<-,SeqExpressionSet,ANY-method, offst<-,SeqExpressionSet-method
● 1 images

barplot-methods (Package: EDASeq) : Methods for Function code{barplot

High-level functions to produce barplots of some complex objects.

● Data Source: BioConductor
● Keywords: methods
● Alias: barplot,BamFile-method, barplot,BamFileList-method, barplot,FastqFileList-method, barplot-methods
● 0 images

betweenLaneNormalization-methods (Package: EDASeq) : Methods for Function code{betweenLaneNormalization

Between-lane normalization for sequencing depth and possibly other distributional differences between lanes.

● Data Source: BioConductor
● Keywords: methods
● Alias: betweenLaneNormalization, betweenLaneNormalization,SeqExpressionSet-method, betweenLaneNormalization,matrix-method, betweenLaneNormalization-methods
● 0 images

biasBoxplot-methods (Package: EDASeq) : Methods for Function code{biasBoxplot

biasBoxplot produces a boxplot representing the distribution of a quantity of interest (e.g. gene counts, log-fold-changes, ...) stratified by a covariate (e.g. gene length, GC-contet, ...).

● Data Source: BioConductor
● Keywords: methods
● Alias: biasBoxplot, biasBoxplot,numeric,numeric,numeric-method, biasBoxplot,numeric,numeric-method, biasBoxplot-methods
● 1 images

biasPlot-methods (Package: EDASeq) : Methods for Function code{biasPlot

biasPlot produces a plot of the lowess regression of the counts on a covariate of interest, tipically the GC-content or the length of the genes.

● Data Source: BioConductor
● Keywords: methods
● Alias: biasPlot, biasPlot,SeqExpressionSet,character-method, biasPlot,matrix,numeric-method, biasPlot-methods
● 1 images

boxplot-methods (Package: EDASeq) : Methods for Function code{boxplot

High-level functions to produce boxplots of some complex objects.

● Data Source: BioConductor
● Keywords: methods
● Alias: boxplot,FastqQuality-method, boxplot,SeqExpressionSet-method, boxplot-methods
● 0 images

getGeneLengthAndGCContent (Package: EDASeq) : Get gene length and GC-content

Automatically retrieves gene length and GC-content information from Biomart or org.db packages.

● Data Source: BioConductor
● Keywords:
● Alias: getGeneLengthAndGCContent
● 0 images

meanVarPlot-methods (Package: EDASeq) : Methods for Function code{meanVarPlot

meanVarPlot produces a smoothScatter plot of the mean variance relation.

● Data Source: BioConductor
● Keywords: methods
● Alias: meanVarPlot, meanVarPlot,SeqExpressionSet-method, meanVarPlot-methods
● 0 images