Package: limorhyde2 0.1.1
Jake Hughey
limorhyde2: Quantify Rhythmicity and Differential Rhythmicity in Genomic Data
Fit linear models based on periodic splines, moderate model coefficients using multivariate adaptive shrinkage, then compute properties of the moderated curves.
Authors:
limorhyde2_0.1.1.tar.gz
limorhyde2_0.1.1.zip(r-4.7)limorhyde2_0.1.1.zip(r-4.6)limorhyde2_0.1.1.zip(r-4.5)
limorhyde2_0.1.1.tgz(r-4.6-any)limorhyde2_0.1.1.tgz(r-4.5-any)
limorhyde2_0.1.1.tar.gz(r-4.7-any)limorhyde2_0.1.1.tar.gz(r-4.6-any)
limorhyde2_0.1.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
limorhyde2/json (API)
NEWS
| # Install 'limorhyde2' in R: |
| install.packages('limorhyde2', repos = c('https://hugheylab.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/hugheylab/limorhyde2/issues
Pkgdown/docs site:https://limorhyde2.hugheylab.org
Last updated from:5a4b8bba9b. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 191 | ||
| source / vignettes | OK | 241 | ||
| linux-release-x86_64 | OK | 188 | ||
| macos-release-arm64 | OK | 97 | ||
| macos-oldrel-arm64 | OK | 96 | ||
| windows-devel | OK | 312 | ||
| windows-release | OK | 157 | ||
| windows-oldrel | OK | 117 | ||
| wasm-release | OK | 136 |
Exports:getDiffRhythmStatsgetExpectedMeasgetExpectedMeasIntervalsgetModelFitgetPosteriorFitgetPosteriorSamplesgetRhythmStatsgetStatsIntervalsmergeMeasMeta
Dependencies:abindashrassertthatbackportsBHBiobaseBiocGenericsBiocParallelcheckmateclicodetoolscpp11data.tableDelayedArrayDESeq2etrunctfarverforeachformatRfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegtableHDIntervalinvgammaIRangesirlbaisobanditeratorslabelinglambda.rlatticelifecyclelimmalocfitmashrMatrixMatrixGenericsmatrixStatsmixsqpmvtnormpbsplyrR6RColorBrewerRcppRcppArmadilloRcppGSLrlangrmetaS4ArraysS4VectorsS7scalesSeqinfosnowsoftImputeSparseArraySQUAREMstatmodSummarizedExperimenttruncnormvctrsviridisLitewithrXVectorzeallot
Analyzing RNA-seq data
Rendered fromrnaseq.Rmdusingknitr::rmarkdownon May 21 2026.Last update: 2022-04-11
Started: 2022-01-27
Quantifying differential rhythmicity between conditions
Rendered fromdifferential-rhythmicity.Rmdusingknitr::rmarkdownon May 21 2026.Last update: 2026-01-20
Started: 2021-07-19
Quantifying rhythmicity in one condition
Rendered fromrhythmicity.Rmdusingknitr::rmarkdownon May 21 2026.Last update: 2026-01-20
Started: 2021-07-19
Quantifying uncertainty in (differential) rhythmicity
Rendered fromuncertainty.Rmdusingknitr::rmarkdownon May 21 2026.Last update: 2026-01-20
Started: 2021-07-19
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Compute differential rhythm statistics from fitted models | getDiffRhythmStats |
| Compute expected measurements from fitted models | getExpectedMeas |
| Compute credible intervals for expected measurements | getExpectedMeasIntervals |
| Fit linear models for rhythmicity in one or more conditions | getModelFit |
| Compute posterior fit for linear models for rhythmicity | getPosteriorFit |
| Draw samples from posterior distributions of fitted models | getPosteriorSamples |
| Compute rhythm statistics from fitted models | getRhythmStats |
| Compute credible intervals for rhythm or differential rhythm statistics | getStatsIntervals |
| Gene expression data for GSE34018 | GSE34018 |
| Gene expression data for GSE54650 | GSE54650 |
| Merge measurements and metadata | mergeMeasMeta |
