subSeq: Subsampling of high-throughput sequencing count data
Version 1.6.0

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

AuthorDavid Robinson, John D. Storey, with contributions from Andrew J. Bass
Bioconductor views DifferentialExpression GeneExpression RNASeq Sequencing Transcription
Date of publicationNone
MaintainerAndrew J. Bass <ajbass@princeton.edu>, John D. Storey <jstorey@princeton.edu>
LicenseMIT + file LICENSE
Version1.6.0
URL http://github.com/StoreyLab/subSeq
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("subSeq")

Getting started

README.md

Popular man pages

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

All man pages Function index File listing

Man pages

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

Functions

DESeq2 Source code
DEXSeq Source code
ccc Source code
combineSubsamples Man page Source code
edgeR Source code
edgeR.glm Source code
g_legend Source code
generateSubsampledMatrix Man page Source code
getSeed Man page Source code
hammer Man page
plot.subsamples Man page Source code
plot.summary.subsamples Man page Source code
qvalue.filtered1 Source code
ss Man page
subsample Man page Source code
subsample.plot.helper Source code
summary.subsamples Man page Source code
voomLimma Source code

Files

DESCRIPTION
LICENSE
NAMESPACE
NEWS
R
R/combineSubsamples.R
R/generateSubsampledMatrix.R
R/hammer-data.R
R/handlers.R
R/plot.summary.subsamples.R
R/subsample.R
R/summary.subsamples.R
README.md
build
build/vignette.rds
data
data/datalist
data/hammer.rda
data/ss.rda
inst
inst/doc
inst/doc/subSeq.R
inst/doc/subSeq.Rnw
inst/doc/subSeq.pdf
man
man/combineSubsamples.Rd
man/generateSubsampledMatrix.Rd
man/getSeed.Rd
man/hammer.Rd
man/plot.subsamples.Rd
man/plot.summary.subsamples.Rd
man/ss.Rd
man/subsample.Rd
man/summary.subsamples.Rd
vignettes
vignettes/refs.bib
vignettes/subSeq.Rnw
subSeq documentation built on May 20, 2017, 9:56 p.m.

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