subSeq v1.2.2

by Andrew J Bass

Subsampling of high-throughput sequencing count data

Subsampling of high throughput sequencing count data for use in experiment design and analysis.

Functions in subSeq

Name	Description
combineSubsamples	combine multiple subsamples objects
subsample	Subsample reads and perform statistical testing on each sample
plot.subsamples	plot metrics as a function of subsampled read depth
getSeed	Extract the global random seed from a subsamples object
hammer	ExpressionSet results from Hammer et al 2010
summary.subsamples	calculate summary statistics for each subsampled depth in a subsamples object
ss	Subsampling results using the hammer dataset
plot.summary.subsamples	plot metrics as a function of subsampled read depth
generateSubsampledMatrix	Generate the read matrix corresponding to a particular level
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Details

Type	Package
biocViews	Sequencing, Transcription, RNASeq, GeneExpression, DifferentialExpression
VignetteBuilder	knitr
URL	http://github.com/StoreyLab/subSeq
License	MIT + file LICENSE
NeedsCompilation	no

depends	base (>= 3.2) , R (>= 3.2)
imports	Biobase , data , data.table , digest , dplyr , ggplot2 , magrittr , qvalue (>= 1.99) , tidyr
suggests	DESeq2 , DEXSeq (>= 1.9.7) , edgeR , knitr , limma , testthat
Contributors	David Robinson, John Storey

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