Package: splineTimeR 1.35.0
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_1.35.0.tar.gz
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splineTimeR_1.35.0.tgz(r-4.5-any)splineTimeR_1.35.0.tgz(r-4.4-any)splineTimeR_1.35.0.tgz(r-4.3-any)
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splineTimeR.pdf |splineTimeR.html✨
splineTimeR/json (API)
NEWS
| # Install 'splineTimeR' in R: |
| install.packages('splineTimeR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- TCsimData - Simulated time-course gene expression data set
On BioConductor:splineTimeR-1.35.0(bioc 3.21)splineTimeR-1.34.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
geneexpressiondifferentialexpressiontimecourseregressiongenesetenrichmentnetworkenrichmentnetworkinferencegraphandnetwork
Last updated 5 months agofrom:3853c2f00c. Checks:1 OK, 7 NOTE. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Feb 28 2025 |
| R-4.5-win | NOTE | Feb 28 2025 |
| R-4.5-mac | NOTE | Feb 28 2025 |
| R-4.5-linux | NOTE | Feb 28 2025 |
| R-4.4-win | NOTE | Feb 28 2025 |
| R-4.4-mac | NOTE | Feb 28 2025 |
| R-4.3-win | NOTE | Feb 28 2025 |
| R-4.3-mac | NOTE | Feb 28 2025 |
Exports:networkPropertiespathEnrichsplineDiffExprssplineNetReconsplinePlot
Dependencies:annotateAnnotationDbiaskpassBiobaseBiocGenericsBiostringsbitbit64blobcachemclicorpcorcpp11crayoncurlDBIfastmapfdrtoolFIsGeneNetgenericsGenomeInfoDbGenomeInfoDbDatagluegraphGSEABasegtoolshttrigraphIRangesjsonliteKEGGRESTlatticelifecyclelimmalongitudinalmagrittrMatrixmemoisemimeopensslpkgconfigplogrpngR6rlangRSQLiteS4VectorsstatmodsysUCSC.utilsvctrsXMLxtableXVector
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 |