Package: splineTimeR 1.33.0

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:Agata Michna

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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'))

Datasets:

TCsimData - Simulated time-course gene expression data set

On BioConductor:splineTimeR-1.33.0(bioc 3.20)splineTimeR-1.32.0(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

5 exports 0.82 score 55 dependencies 3 mentions

Last updated 2 months agofrom:5dfc68a1e2

Exports:networkProperties pathEnrich splineDiffExprs splineNetRecon splinePlot

Dependencies:annotate AnnotationDbi askpass Biobase BiocGenerics Biostrings bit bit64 blob cachem cli corpcor cpp11 crayon curl DBI fastmap fdrtool FIs GeneNet GenomeInfoDb GenomeInfoDbData glue graph GSEABase gtools httr igraph IRanges jsonlite KEGGREST lattice lifecycle limma longitudinal magrittr Matrix memoise mime openssl pkgconfig plogr png R6 rlang RSQLite S4Vectors statmod sys UCSC.utils vctrs XML xtable XVector zlibbioc

splineTimeR

Rendered fromsplineTimeR.Rnwusingutils::Sweaveon Jun 12 2024.

Last update: 2016-10-05
Started: 2016-03-25

Citation

Development and contributors

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