Package: Rnits 1.47.0

Dipen P. Sangurdekar

Rnits: R Normalization and Inference of Time Series data

R/Bioconductor package for normalization, curve registration and inference in time course gene expression data.

Authors:Dipen P. Sangurdekar <[email protected]>

Rnits_1.47.0.tar.gz
Rnits_1.47.0.zip(r-4.7)Rnits_1.47.0.zip(r-4.6)Rnits_1.47.0.zip(r-4.5)
Rnits_1.47.0.tgz(r-4.6-any)Rnits_1.47.0.tgz(r-4.5-any)
Rnits_1.47.0.tar.gz(r-4.7-any)Rnits_1.47.0.tar.gz(r-4.6-any)
Rnits_1.47.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
Rnits/json (API)
NEWS

# Install 'Rnits' in R:
install.packages('Rnits', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:

On BioConductor:Rnits-1.47.0(bioc 3.24)Rnits-1.46.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

geneexpressionmicroarraytimecoursedifferentialexpressionnormalization

4.00 score 3 scripts 334 downloads 14 exports 35 dependencies

Last updated from:e2d32d6842. Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR179
linux-devel-x86_64WARNING192
source / vignettesOK318
linux-release-x86_64WARNING199
macos-release-arm64WARNING131
macos-oldrel-arm64WARNING126
windows-develWARNING113
windows-releaseWARNING138
windows-oldrelWARNING176
wasm-releaseOK127

Exports:build.RnitscalculateGCVfitgetCIDgetFitModelgetLRgetNormTwoChannelgetPvalgetStatplotResultssummarizeProbessummarytimeAligntopData

Dependencies:affyaffyioBiobaseBiocGenericsBiocManagerbootclicpp11farvergenericsggplot2gluegtableimputeisobandlabelinglifecyclelimmamagrittrplyrpreprocessCoreqvalueR6RColorBrewerRcppreshape2rlangS7scalesstatmodstringistringrvctrsviridisLitewithr

R/Bioconductor package for normalization and differential expression inference in time series gene expression microarray data.

Rendered fromRnits-vignette.Rnwusingknitr::knitron Jun 03 2026.

Last update: 2019-03-17
Started: 2014-09-05

Readme and manuals

Help Manual

Help pageTopics
replace slot of Rnits$ $<-,Rnits-method
Input the RGlist raw data, build a Rnits object and perform filtering and normalizationbuild.Rnits
Calculate the optimal B-spline model using generalized cross-validationcalculateGCV calculateGCV,character,ANY-method calculateGCV,Rnits-method
Fit model on time series datafit fit,character,ANY-method fit,Rnits-method
Cluster IDs of probes/genes from fitted 'Rnits'getCID getCID,character,ANY-method getCID,Rnits-method
Extract fit data from 'Rnits' objectgetFitModel getFitModel,character,ANY-method getFitModel,Rnits-method
Get log-ratiosgetLR getLR,character,ANY-method getLR,Rnits-method Rnits.getLR
Get Normalized channel data for two channel arraysgetNormTwoChannel getNormTwoChannel,character,ANY-method getNormTwoChannel,Rnits-method
Get p-valuesgetPval getPval,character,ANY-method getPval,Rnits-method
Retrieve ratio statisticsgetStat getStat,character,ANY-method getStat,Rnits-method
Plot profiles of top genes/probesplotResults plotResults,character,ANY-method plotResults,Rnits-method
rnits.rnits-package rnits
rnits classRnits-class
Summarize probe level data to gene level datasummarizeProbes summarizeProbes,character,ANY-method summarizeProbes,Rnits-method
Summary of fitsummary,Rnits-method
Curve registration of time series curvestimeAlign timeAlign,character,ANY-method timeAlign,Rnits-method
Data of top genes/probestopData topData,character,ANY-method topData,Rnits-method
Yeast chemostat data from Ronen and Botstein (Proc Natl Acad Sci U S A. 2006 Jan 10;103(2):389-94. Epub 2005 Dec 28.)yeastchemostat