NanoStringDiff: Differential Expression Analysis of NanoString nCounter Data

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>
Date of publicationNone
Maintainerhong wang <hong.wang@uky.edu>
LicenseGPL
Version1.4.0

View on Bioconductor

Functions

createNanoStringSet Man page
createNanoStringSetFromCsv Man page
estNormalizationFactors Man page
estNormalizationFactors,estNormalizationFactors-method Man page
glm.LRT Man page
glm.LRT,NanoStringSet-method Man page
housekeepingControl Man page
housekeepingControl<- Man page
housekeepingControl<-,NanoStringSet,matrix-method Man page
housekeepingControl,NanoStringSet-method Man page
housekeepingFactor Man page
housekeepingFactor<- Man page
housekeepingFactor,NanoStringSet-method Man page
housekeepingFactor<-,NanoStringSet,numeric-method Man page
NanoStringData Man page
NanoStringDiff Man page
NanoStringDiff-package Man page
NanoStringSet Man page
NanoStringSet-class Man page
negativeControl Man page
negativeControl<- Man page
negativeControl<-,NanoStringSet,matrix-method Man page
negativeControl,NanoStringSet-method Man page
negativeFactor Man page
negativeFactor<- Man page
negativeFactor,NanoStringSet-method Man page
negativeFactor<-,NanoStringSet,numeric-method Man page
positiveControl Man page
positiveControl<- Man page
positiveControl<-,NanoStringSet,matrix-method Man page
positiveControl,NanoStringSet-method Man page
positiveFactor Man page
positiveFactor<- Man page
positiveFactor,NanoStringSet-method Man page
positiveFactor<-,NanoStringSet,numeric-method Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.