Package: Rnits 1.41.0
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:
Rnits_1.41.0.tar.gz
Rnits_1.41.0.zip(r-4.5)Rnits_1.41.0.zip(r-4.4)Rnits_1.41.0.zip(r-4.3)
Rnits_1.41.0.tgz(r-4.4-any)Rnits_1.41.0.tgz(r-4.3-any)
Rnits_1.41.0.tar.gz(r-4.5-noble)Rnits_1.41.0.tar.gz(r-4.4-noble)
Rnits_1.41.0.tgz(r-4.4-emscripten)Rnits_1.41.0.tgz(r-4.3-emscripten)
Rnits.pdf |Rnits.html✨
Rnits/json (API)
NEWS
| # Install 'Rnits' in R: |
| install.packages('Rnits', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- yeastchemostat - Yeast chemostat data from Ronen and Botstein
On BioConductor:Rnits-1.41.0(bioc 3.21)Rnits-1.40.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
geneexpressionmicroarraytimecoursedifferentialexpressionnormalization
Last updated 2 months agofrom:4df67b12ba. Checks:OK: 1 WARNING: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 18 2024 |
| R-4.5-win | WARNING | Nov 18 2024 |
| R-4.5-linux | WARNING | Dec 18 2024 |
| R-4.4-win | WARNING | Nov 18 2024 |
| R-4.4-mac | WARNING | Dec 18 2024 |
| R-4.3-win | WARNING | Nov 18 2024 |
| R-4.3-mac | WARNING | Dec 18 2024 |
Exports:build.RnitscalculateGCVfitgetCIDgetFitModelgetLRgetNormTwoChannelgetPvalgetStatplotResultssummarizeProbessummarytimeAligntopData
Dependencies:affyaffyioBiobaseBiocGenericsBiocManagerbootclicolorspacefansifarvergenericsggplot2gluegtableimputeisobandlabelinglatticelifecyclelimmamagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigplyrpreprocessCoreqvalueR6RColorBrewerRcppreshape2rlangscalesstatmodstringistringrtibbleutf8vctrsviridisLitewithrzlibbioc
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 |
