Rnits: R Normalization and Inference of Time Series data

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

Author
Dipen P. Sangurdekar <dipen.sangurdekar@gmail.com>
Date of publication
None
Maintainer
Dipen P. Sangurdekar <dipen.sangurdekar@gmail.com>
License
GPL-3
Version
1.8.0

View on Bioconductor

Man pages

build.Rnits
Input the RGlist raw data, build a Rnits object and perform...
calculateGCV-methods
Calculate the optimal B-spline model using generalized...
extract-methods
replace slot of Rnits
fit-methods
Fit model on time series data
getCID-methods
Cluster IDs of probes/genes from fitted 'Rnits'
getFitModel-methods
Extract fit data from 'Rnits' object
getLR-methods
Get log-ratios
getNormTwoChannel-methods
Get Normalized channel data for two channel arrays
getPval-methods
Get p-values
getStat-methods
Retrieve ratio statistics
plotResults-methods
Plot profiles of top genes/probes
rnits
rnits.
Rnits-class
rnits class
summarizeProbes-methods
Summarize probe level data to gene level data
summary-methods
Summary of fit
timeAlign-methods
Curve registration of time series curves
topData-methods
Data of top genes/probes
yeastchemostat
Yeast chemostat data from Ronen and Botstein (Proc Natl Acad...

Files in this package

Rnits/DESCRIPTION
Rnits/NAMESPACE
Rnits/R
Rnits/R/AllClasses.R
Rnits/R/build-rnits.r
Rnits/R/calculate-gcv.r
Rnits/R/fit.r
Rnits/R/getFitModel.r
Rnits/R/getLR.r
Rnits/R/getcid.r
Rnits/R/getnormtwochannel.r
Rnits/R/getpval.r
Rnits/R/getstat.r
Rnits/R/misc-functions.r
Rnits/R/plotresults.r
Rnits/R/rnits-package.r
Rnits/R/summarize-probes.r
Rnits/R/summary.r
Rnits/R/timealign.r
Rnits/R/topdata.r
Rnits/R/yeastchemostat-data.r
Rnits/README.md
Rnits/build
Rnits/build/vignette.rds
Rnits/data
Rnits/data/yeastchemostat.rda
Rnits/inst
Rnits/inst/NEWS
Rnits/inst/doc
Rnits/inst/doc/Rnits-vignette.R
Rnits/inst/doc/Rnits-vignette.Rnw
Rnits/inst/doc/Rnits-vignette.pdf
Rnits/man
Rnits/man/Rnits-class.Rd
Rnits/man/build.Rnits.Rd
Rnits/man/calculateGCV-methods.Rd
Rnits/man/extract-methods.Rd
Rnits/man/fit-methods.Rd
Rnits/man/getCID-methods.Rd
Rnits/man/getFitModel-methods.Rd
Rnits/man/getLR-methods.Rd
Rnits/man/getNormTwoChannel-methods.Rd
Rnits/man/getPval-methods.Rd
Rnits/man/getStat-methods.Rd
Rnits/man/plotResults-methods.Rd
Rnits/man/rnits.Rd
Rnits/man/summarizeProbes-methods.Rd
Rnits/man/summary-methods.Rd
Rnits/man/timeAlign-methods.Rd
Rnits/man/topData-methods.Rd
Rnits/man/yeastchemostat.Rd
Rnits/vignettes
Rnits/vignettes/Bibliography.bib
Rnits/vignettes/Rnits-vignette.Rnw