Package: Rnits 1.39.0

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]>

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Rnits.pdf |Rnits.html✨
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NEWS

# Install 'Rnits' in R:

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

Datasets:

yeastchemostat - Yeast chemostat data from Ronen and Botstein

On BioConductor:Rnits-1.39.0(bioc 3.20)Rnits-1.38.0(bioc 3.19)

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

bioconductor-package

14 exports 0.91 score 45 dependencies

Last updated 2 months agofrom:d4219b602c

Exports:build.Rnits calculateGCV fit getCID getFitModel getLR getNormTwoChannel getPval getStat plotResults summarizeProbes summary timeAlign topData

Dependencies:affy affyio Biobase BiocGenerics BiocManager boot cli colorspace fansi farver ggplot2 glue gtable impute isoband labeling lattice lifecycle limma magrittr MASS Matrix mgcv munsell nlme pillar pkgconfig plyr preprocessCore qvalue R6 RColorBrewer Rcpp reshape2 rlang scales statmod stringi stringr tibble utf8 vctrs viridisLite withr zlibbioc

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

Rendered fromRnits-vignette.Rnwusingknitr::knitron Jun 17 2024.

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
replace slot of Rnits	$ $<-,Rnits-method
Input the RGlist raw data, build a Rnits object and perform filtering and normalization	build.Rnits
Calculate the optimal B-spline model using generalized cross-validation	calculateGCV calculateGCV,character,ANY-method calculateGCV,Rnits-method
Fit model on time series data	fit 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' object	getFitModel getFitModel,character,ANY-method getFitModel,Rnits-method
Get log-ratios	getLR getLR,character,ANY-method getLR,Rnits-method Rnits.getLR
Get Normalized channel data for two channel arrays	getNormTwoChannel getNormTwoChannel,character,ANY-method getNormTwoChannel,Rnits-method
Get p-values	getPval getPval,character,ANY-method getPval,Rnits-method
Retrieve ratio statistics	getStat getStat,character,ANY-method getStat,Rnits-method
Plot profiles of top genes/probes	plotResults plotResults,character,ANY-method plotResults,Rnits-method
rnits.	rnits-package rnits
rnits class	Rnits-class
Summarize probe level data to gene level data	summarizeProbes summarizeProbes,character,ANY-method summarizeProbes,Rnits-method
Summary of fit	summary,Rnits-method
Curve registration of time series curves	timeAlign timeAlign,character,ANY-method timeAlign,Rnits-method
Data of top genes/probes	topData 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