NanoStringDiff: Differential Expression Analysis of NanoString nCounter Data
Version 1.6.0

This Package utilizes a generalized linear model(GLM) of the negative binomial family to characterize count data and allows for multi-factor design. NanoStrongDiff incorporate size factors, calculated from positive controls and housekeeping controls, and background level, obtained from negative controls, in the model framework so that all the normalization information provided by NanoString nCounter Analyzer is fully utilized.

Authorhong wang <hong.wang@uky.edu>, chi wang <chi.wang@uky.edu>
Bioconductor views DifferentialExpression Normalization
Date of publicationNone
Maintainerhong wang <hong.wang@uky.edu>
LicenseGPL
Version1.6.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("NanoStringDiff")

Getting started

Package overview

Popular man pages

estNormalizationFactors: estimate normalization factors,include positive size factors,...
glm.LRT: perform gene-wise likelihood ratio test for NanoString Data
housekeepingFactor: Acessor functions for the 'housekeepingFactor' slot in a...
NanoStringDiff-package: NanoStringDiff package for differential expression analysis...
negativeControl: Acessor functions for the 'negativeControl' slot in a...
positiveControl: Acessor functions for the 'positiveControl' slot in a...
positiveFactor: Acessor functions for the 'positiveFactor' slot in a...
See all...

All man pages Function index File listing

Man pages

estNormalizationFactors: estimate normalization factors,include positive size factors,...
glm.LRT: perform gene-wise likelihood ratio test for NanoString Data
housekeepingControl: Acessor functions for the 'housekeepingControl' slot in a...
housekeepingFactor: Acessor functions for the 'housekeepingFactor' slot in a...
NanoStringData: A real 'NanoStringSet' object.
NanoStringDiff-class: NanoStringSet object and constructors
NanoStringDiff-package: NanoStringDiff package for differential expression analysis...
negativeControl: Acessor functions for the 'negativeControl' slot in a...
negativeFactor: Acessor functions for the 'negativeFactor' slot in a...
positiveControl: Acessor functions for the 'positiveControl' slot in a...
positiveFactor: Acessor functions for the 'positiveFactor' slot in a...

Functions

NanoStringData Man page
NanoStringDiff Man page
NanoStringDiff-package Man page
NanoStringSet Man page
NanoStringSet-class Man page
compute.baseSigma Source code
createNanoStringSet Man page Source code
createNanoStringSetFromCsv Man page Source code
est.dispersion Source code
estNormalizationFactors Man page Source code
estNormalizationFactors,estNormalizationFactors-method Man page
glm.LRT Man page Source code
glm.LRT,NanoStringSet-method Man page
glmfit.OneGroup Source code
glmfit.full Source code
glmfit.reduce Source code
housekeepingControl Man page
housekeepingControl,NanoStringSet-method Man page
housekeepingControl<- Man page
housekeepingControl<-,NanoStringSet,matrix-method Man page
housekeepingFactor Man page
housekeepingFactor,NanoStringSet-method Man page
housekeepingFactor<- Man page
housekeepingFactor<-,NanoStringSet,numeric-method Man page
negativeControl Man page
negativeControl,NanoStringSet-method Man page
negativeControl<- Man page
negativeControl<-,NanoStringSet,matrix-method Man page
negativeFactor Man page
negativeFactor,NanoStringSet-method Man page
negativeFactor<- Man page
negativeFactor<-,NanoStringSet,numeric-method Man page
positiveControl Man page
positiveControl,NanoStringSet-method Man page
positiveControl<- Man page
positiveControl<-,NanoStringSet,matrix-method Man page
positiveFactor Man page
positiveFactor,NanoStringSet-method Man page
positiveFactor<- Man page
positiveFactor<-,NanoStringSet,numeric-method Man page
rnegbinom Source code

Files

DESCRIPTION
NAMESPACE
R
R/AllClass.R
R/estNormalizationFactors.R
R/glm_LRT.R
R/util.R
build
build/vignette.rds
data
data/NanoStringData.rda
inst
inst/NEWS
inst/doc
inst/doc/NanoStringDiff.R
inst/doc/NanoStringDiff.Rnw
inst/doc/NanoStringDiff.pdf
inst/extdata
inst/extdata/Mori.csv
man
man/NanoStringData.Rd
man/NanoStringDiff-class.Rd
man/NanoStringDiff-package.Rd
man/estNormalizationFactors.Rd
man/glm.LRT.Rd
man/housekeepingControl.Rd
man/housekeepingFactor.Rd
man/negativeControl.Rd
man/negativeFactor.Rd
man/positiveControl.Rd
man/positiveFactor.Rd
tests
tests/testthat
tests/testthat.R
tests/testthat/test_createNanoStringSet.R
tests/testthat/test_estNormalizationFactors.R
tests/testthat/test_glmLRT.R
vignettes
vignettes/Bioconductor.sty
vignettes/NanoStringDiff.Rnw
vignettes/example.PNG
vignettes/reference.bib
vignettes/unsrturl.bst
NanoStringDiff documentation built on May 20, 2017, 10:51 p.m.

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