1 Citation | 2 Quick Start | 3 Data Input | 4 Differential Expression Analysis for Single Factor Experiment | 5 Differential Expression Analysis for Multifactor Experiment | 6 Session Info
Package: NanoStringDiff 1.43.0
tingting zhai
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.
Authors:
NanoStringDiff_1.43.0.tar.gz
NanoStringDiff_1.43.0.zip(r-4.7)NanoStringDiff_1.43.0.zip(r-4.6)NanoStringDiff_1.43.0.zip(r-4.5)
NanoStringDiff_1.43.0.tgz(r-4.6-x86_64)NanoStringDiff_1.43.0.tgz(r-4.6-arm64)NanoStringDiff_1.43.0.tgz(r-4.5-x86_64)NanoStringDiff_1.43.0.tgz(r-4.5-arm64)
NanoStringDiff_1.43.0.tar.gz(r-4.7-arm64)NanoStringDiff_1.43.0.tar.gz(r-4.7-x86_64)NanoStringDiff_1.43.0.tar.gz(r-4.6-arm64)NanoStringDiff_1.43.0.tar.gz(r-4.6-x86_64)
NanoStringDiff_1.43.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
NanoStringDiff/json (API)
| # Install 'NanoStringDiff' in R: |
| install.packages('NanoStringDiff', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- NanoStringData - A real 'NanoStringSet' object.
On BioConductor:NanoStringDiff-1.43.0(bioc 3.24)NanoStringDiff-1.42.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
differentialexpressionnormalizationcpp
Last updated from:2ce8dd13b1. Checks:1 ERROR, 11 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 151 | ||
| linux-devel-arm64 | WARNING | 192 | ||
| linux-devel-x86_64 | WARNING | 210 | ||
| source / vignettes | OK | 191 | ||
| linux-release-arm64 | WARNING | 181 | ||
| linux-release-x86_64 | WARNING | 214 | ||
| macos-release-arm64 | WARNING | 166 | ||
| macos-release-x86_64 | WARNING | 318 | ||
| macos-oldrel-arm64 | WARNING | 122 | ||
| macos-oldrel-x86_64 | WARNING | 218 | ||
| windows-devel | WARNING | 293 | ||
| windows-release | WARNING | 221 | ||
| windows-oldrel | WARNING | 227 | ||
| wasm-release | OK | 123 |
Exports:compute.baseSigmacreateNanoStringSetcreateNanoStringSetFromCsvest.dispersionestNormalizationFactorsfun5glm.LRTglmfit.fullglmfit.OneGroupglmfit.reducehousekeepingControlhousekeepingControl<-housekeepingFactorhousekeepingFactor<-NanoStringDataNormalizationnegativeControlnegativeControl<-negativeFactornegativeFactor<-PlotsPositiveHousekeepingpositiveControlpositiveControl<-positiveFactorpositiveFactor<-rnegbinom
Dependencies:BiobaseBiocGenericsgenericsmatrixStatsRcpp
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| A short title line describing what the package does | NanoStringDiff-package NanoStringDiff |
| estimate normalization factors,include positive size factors, background noise, housekeeping size factors. | estNormalizationFactors estNormalizationFactors,estNormalizationFactors-method |
| perform gene-wise likelihood ratio test for NanoString Data | glm.LRT glm.LRT,NanoStringSet-method |
| Acessor functions for the 'housekeepingControl' slot in a NanoStringSet object. | housekeepingControl housekeepingControl,NanoStringSet-method housekeepingControl<- housekeepingControl<-,NanoStringSet,matrix-method |
| Acessor functions for the 'housekeepingFactor' slot in a NanoStringSet object. | housekeepingFactor housekeepingFactor,NanoStringSet-method housekeepingFactor<- housekeepingFactor<-,NanoStringSet,numeric-method |
| A real 'NanoStringSet' object. | NanoStringData |
| Normalize NanoStringData | NanoStringDataNormalization NanoStringDataNormalization,NanoStringDataNormalization-method |
| NanoStringSet object and constructors | createNanoStringSet createNanoStringSetFromCsv NanoStringSet NanoStringSet-class |
| Acessor functions for the 'negativeControl' slot in a NanoStringSet object. | negativeControl negativeControl,NanoStringSet-method negativeControl<- negativeControl<-,NanoStringSet,matrix-method |
| Acessor functions for the 'negativeFactor' slot in a NanoStringSet object. | negativeFactor negativeFactor,NanoStringSet-method negativeFactor<- negativeFactor<-,NanoStringSet,numeric-method |
| Plots of positive controls and housekeeping genes | PlotsPositiveHousekeeping PlotsPositiveHousekeeping,PlotsPositiveHousekeeping-method |
| Acessor functions for the 'positiveControl' slot in a NanoStringSet object. | positiveControl positiveControl,NanoStringSet-method positiveControl<- positiveControl<-,NanoStringSet,matrix-method |
| Acessor functions for the 'positiveFactor' slot in a NanoStringSet object. | positiveFactor positiveFactor,NanoStringSet-method positiveFactor<- positiveFactor<-,NanoStringSet,numeric-method |