NanoStringDiff: Differential Expression Analysis of NanoString nCounter Data

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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.

Author
hong wang <hong.wang@uky.edu>, chi wang <chi.wang@uky.edu>
Date of publication
None
Maintainer
hong wang <hong.wang@uky.edu>
License
GPL
Version
1.4.0

View on Bioconductor

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...

Files in this package

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