Overview | Data preparation | Time-course data differential expression analysis | Visualization of time-course data with natural cubic spline regression model | Pathway enrichment analysis | Gene association network reconstruction of time-course data | Scale-free properties of a network
Package: splineTimeR 1.41.0
Herbert Braselmann
splineTimeR: Time-course differential gene expression data analysis using spline regression models followed by gene association network reconstruction
This package provides functions for differential gene expression analysis of gene expression time-course data. Natural cubic spline regression models are used. Identified genes may further be used for pathway enrichment analysis and/or the reconstruction of time dependent gene regulatory association networks.
Authors:
splineTimeR_1.41.0.tar.gz
splineTimeR_1.41.0.zip(r-4.7)splineTimeR_1.41.0.zip(r-4.6)splineTimeR_1.41.0.zip(r-4.5)
splineTimeR_1.41.0.tgz(r-4.6-any)splineTimeR_1.41.0.tgz(r-4.5-any)
splineTimeR_1.41.0.tar.gz(r-4.7-any)splineTimeR_1.41.0.tar.gz(r-4.6-any)
splineTimeR_1.41.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
splineTimeR/json (API)
| # Install 'splineTimeR' in R: |
| install.packages('splineTimeR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- TCsimData - Simulated time-course gene expression data set
On BioConductor:splineTimeR-1.41.0(bioc 3.24)splineTimeR-1.40.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
geneexpressiondifferentialexpressiontimecourseregressiongenesetenrichmentnetworkenrichmentnetworkinferencegraphandnetwork
Last updated from:69a96090b8. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 177 | ||
| linux-devel-x86_64 | NOTE | 271 | ||
| source / vignettes | OK | 258 | ||
| linux-release-x86_64 | NOTE | 252 | ||
| macos-release-arm64 | NOTE | 195 | ||
| macos-oldrel-arm64 | NOTE | 199 | ||
| windows-devel | NOTE | 205 | ||
| windows-release | NOTE | 229 | ||
| windows-oldrel | NOTE | 205 | ||
| wasm-release | OK | 147 |
Exports:networkPropertiespathEnrichsplineDiffExprssplineNetReconsplinePlot
Dependencies:annotateAnnotationDbiaskpassBiobaseBiocGenericsBiostringsbitbit64blobcachemclicorpcorcpp11crayoncurlDBIfastmapfdrtoolFIsGeneNetgenericsgluegraphGSEABasegtoolshttrigraphIRangesjsonliteKEGGRESTlatticelifecyclelimmalongitudinalmagrittrMatrixmemoisemimeopensslpkgconfigpngR6rlangRSQLiteS4VectorsSeqinfostatmodsysvctrsXMLxtableXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Scale-free properties of a network | networkProperties |
| Pathway enrichment analysis | pathEnrich |
| Differential expression analysis based on natural cubic spline regression models for time-course data | splineDiffExprs |
| Network reconstruction based on partial correlation method with shrinkage approach | splineNetRecon |
| Plot spline regression curves of time-course data | splinePlot |
| Simulated time-course gene expression data set | TCsimData |
