subSeq v1.2.2
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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